Science method

Molecular Modeling - Science method

Molecular Modeling are molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules.
Questions related to Molecular Modeling
  • asked a question related to Molecular Modeling
Question
2 answers
Hello everyone,
I docked the inhibitor to the metalloenzyme and the next step was the minimization of the complex. Unfortunately, during the minimization protocol, I got the error as below:
>Solvent file: XXX\bin\Windows-x64\..\..\data\water.slv
>Block specifies desired NFIELD -- accepting block
>RDSOLV: missing params for atom number 36261 (type n2) in .slv file, solvation model 3
>MINI: Error generating interactions
>Problem in minimization of distinct structures.
>Skipping input structure due to forcefield interaction errors.
>BatchMin: normal termination
The atom number 36261 is the Nickel 2+ ion. I've tried to change for the one without charge, but still the OPLSe do not operate with it.
My question is about: how to add the nickel ions to the FF with proper parameters.
Thank you!
Michal
Relevant answer
Answer
Did you fix this error! As I got the same results "RDSOLV: missing params for atom number 1 (type GG) in .slv file, solvation model 3" when trying minimization of Platinum-containing compounds.
  • asked a question related to Molecular Modeling
Question
4 answers
Hi everybody
I am seeking for a molecular modelling package with graphical interface for drawing molecules in Ubuntu. Previously, I have worked with HyperChem and Gaussian in windows. Is there a software similar to HyperChem?
Thank you
Relevant answer
Answer
Thanks for your responces
  • asked a question related to Molecular Modeling
Question
35 answers
Now, I am intrested in the molecular modelling of proteins and one of the most important protein-ligand docking software is Autodock vina so I want to know how can I get free download for windows 10 ? thanks anyway.
Relevant answer
Answer
Dear Dr. @Rukayat Abdulsalam
I'm and my colleague Dr. Nihad are ready for help and we will be glad to do so
  • asked a question related to Molecular Modeling
Question
4 answers
In order to represent our observations or sight of a physical process and to further investigate it by conducting experiments or Numerically models? What are basics one need to focus ? Technically, how one should think? First, thing is understanding, you should be there! If we are modeling a flow we have to be the flow, if representing a let's say a ball, you have to be the ball! To better understand it! What are others?
Relevant answer
Answer
Aditya Kumar Mishra replication is tough though i do agree with the expert comments above that physical replication like visualization is a must one of the important criteria I feel is to To assess applicability one must always specify the requirements along with exact what attribute of a previous results of interest.
  • asked a question related to Molecular Modeling
Question
3 answers
Most pharmacy students rated the use of complex molecular modelling or computational tools as useful for improving engagement and learning outcomes. Further, it significantly improves students' understanding of pharmacological concepts necessary for competency in medication management, based on significant improvements in post-test scores. 
My concern is that if all the above mentioned/stated positive outcomes generated through the use of these pedagogical tools in some ways or other help to reduce the cognitive load or not? Do we have reasons to believe this? I am trying to establish the link between how 2D or 3D visualisation technologies and their relation to cognitive load management.
Relevant answer
Answer
Thanks, Muhammed Yaseen Alzahawi , I am of the same opinion, however, I am more interested in the underlying rationale.
Dear Wajd Alkhawaldeh, thanks for your elaboration on the query. With my limited understanding and what the literature outlined, it depends on the VSA (Visual-spatial abilities) capability of the individuals. Individuals with high VSA are able to process spatially complex procedures while still retaining sufficient cognitive resources to benefit from using 3D visualisation while learning. With low VSA, individuals utilise more cognitive resources when performing a spatially complex task. This results in an increase in cognitive load as they learn. Therefore, in individuals with low VSA, it may be possible to compensate for the higher cognitive demands by improving instructional methods.
  • asked a question related to Molecular Modeling
Question
6 answers
Cannot find any complete set of parameters for Na-Al-Si-O (or sodium aluminosilicates) for ReaxFF. Any help will be very much appreciated. 
Relevant answer
Answer
How does one go about parameterizing the forcefields? I do not seem to be able to find any code used for training/reparameterizing ReaxFF work.
  • asked a question related to Molecular Modeling
Question
5 answers
I trying to install vina using pip and get this error(see file). I think the problem is that boost is not added to path. I have tried various tips posted on stackoverflow threads, read the boost docs for working with python and even watched the videos about how to install boost, but have not been able to solve this problem.
Apart from using pip I tried to install via conda following this manual:
Error not fixed. How i can add boost to path? After installing boost via bootstrap.bat and then .\b2 i get 2 links, but if i add it to PATH variable it doesn't solve this problem. I want to try use Vina scripts in python file
Has anyone been able to install Autodock Vina via pip or conda?
Brief output:
...
ValueError: Boost library location was not found!
Directories searched: conda env, /usr/local/include and /usr/include.
Relevant answer
Answer
Artem Petrov You can use the WSL/WSL2 in Windows to simulate a Linux environment, then you can use conda in it.
  • asked a question related to Molecular Modeling
Question
1 answer
I have performed MD simulation of 100ns on Desmond and now I want to calculate solvent accessible surface (SASA) area over the trajectory. Can Anyone please guide how to do it? Thanking you all in Anticipation.
Relevant answer
Answer
you should generate the data file through the raw data. Automatically software will calculate all the required parameters.
  • asked a question related to Molecular Modeling
Question
3 answers
I have performed a simulation via Desmond, now i want to perform MMPBSA. I dont think Desmond has any functionality of calculating MM/PBSA. I wonder how to move forward? Youre guidance will be highly appreciated.
Thanks
Relevant answer
Answer
Hi, I think you should look into this thread for details:
From "Bowen Tang"
Of course you can do this.
thermal_mmgbsa.py is in $SCHRODINGER/mmshare-vxxxxx/python/common
run it as below:
$SCHRODINGER/run thermal_mmgbsa.py <your_trajectory.cms>
Good luck.
  • asked a question related to Molecular Modeling
Question
4 answers
Actually I am printing unwrapped coordinates of atom but in that output file lot of extra things are written so how I can avoid these things. Is there any inbuilt lammps command. Please help me to overcome this problem #lammps
Relevant answer
Answer
Like Rahul Sahu mentioned above you can use the command in your input file (.in)
dump 1 all custom 100 file.xyz id xu yu zu
dump_modify 1 sort id
where file.xyz is the name of the output file
The second dump modify sort command makes sure atoms are written in same order for every frame. This is useful for easy post processing and data analysis.
  • asked a question related to Molecular Modeling
Question
3 answers
I'm trying to build outer membrane of e. coli with small peptides above it, with CHARMM-gui. Peptides should be positioned above the membrane, but charmm-gui creates space for them between LPS (lipopolisacharides) pushing LPS-s to the edges of simulation box.
If I use only one peptide, it is not problem, empty spaces is not big, and charmm-gui sucessfully finishes job. But when using more peptides, empty space created underneath them is large, so LPS-s are pushed to the edges, tightly packed, which obaviously causes problem for charmm-gui and gives error:
"Charmm terminates abnormally. Please check the output or report this failure to the CHARMM-GUI developers. The bilayer generation is stopped to prevent an infinite loop. Please refresh the browser to restart the bilayer generation with different random seed."
I tried several times, with the same outcome. It looks like membrane builder thinks that peptides are "inserted" in LPS, so it leaves empty space for them in between LPS-s.
I report error to charmm-gui developers, and got short answer: "View “step3_packing.pdb”. "
I looked, and see nothing strange, nothing to lead me to solve the problem.
Any idea where to look, or how to solve problem?
Third picture is outer membrane without peptides
Thanks
Relevant answer
Answer
What about adding your peptides on the other side of the bilayer?
If you are using pbc they should still be able to move over and interact with the LPS. Just be sure to put a good bit of space between them and the inner leaflet.
  • asked a question related to Molecular Modeling
Question
5 answers
Hello.
I am trying to use gromacs to start an MD simulation of a protein-ligand complex.
I was following the recommended tutorial http://www.mdtutorials.com/gmx/complex/index.html
- I did the system preparation, minimization and heating.
- I am trying to start an equilibrium as a continuation from the heating, getting two errors: FATAL ERROR or INCONSISTENCY INPUT.
_____________________________________________________________________________
---> options in my step07_npt.mdp file:
[...]
continuation = yes ; continuing from NVT
[...]
gen_vel = no ; velocity generation off after NVT
_____________________________________________________________________________
running previous grompp to generate tpr.
_____________________________________________________________________________
$ gmx_mpi grompp -f par/mdp/step07a_npt.mdp
-c str/complex/step06d_nvt_ann_LONG.gro
-r str/complex/step06d_nvt_ann_LONG.gro
-p top/top/test.top
-t bin/cpt/step06d_nvt_ann_LONG.cpt
-n str/idx/step06c_complex.ndx
-o bin/tpr/step07a_npt.tpr
-pp top/top/step07a_npt_POSRE.top
-po run/log/mdout/step07a_npt_mdout.mdp
I tried different options:
[ step06_nvt is previous heating step - step07_npt is equilibrium step]
1. try running continuation from heating using heating output files:
_____________________________________________________________________________
$ gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr
-cpi bin/cpt/step06d_nvt_ann_LONG.cpt
-o bin/trj/step06d_nvt_ann_LONG.trr
-x bin/trj/step06d_nvt_ann_LONG.xtc
-cpo bin/cpt/step07a_npt.cpt -cpt 60
-c str/complex/step07a_npt.gro
-e bin/edr/step06d_nvt_ann_LONG.edr
-g run/log/mdlog/step06_nvt_ann_LONG.log
ERROR:
>
Inconsistency in user input:
Some output files listed in the checkpoint file
bin/cpt/step06d_nvt_ann_LONG.cpt are not present or not named as the output
files by the current program:)
Expected output files that are present:
Expected output files that are not present or named differently:
run/log/mdlog/step06_nvt_ann_LONG.log
bin/trj/step06d_nvt_ann_LONG.xtc
bin/edr/step06d_nvt_ann_LONG.edr
To keep your simulation files safe, this simulation will not restart. Either
name your output files exactly the same as the previous simulation part (e.g.
with -deffnm or explicit naming), or make sure all the output files are
present (e.g. run from the same directory as the previous simulation part), or
instruct mdrun to write new output files with mdrun -noappend. In the last
case, you will not be able to use appending in future for this simulation.
_____________________________________________________________________________
2. running with noappend option and using new file names.
_____________________________________________________________________________
$ gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr
-cpi bin/cpt/step06d_nvt_ann_LONG.cpt
-o bin/trj/step07a_npt.trr
-x bin/trj/step07a_npt.xtc
-cpo bin/cpt/step07a_npt.cpt -cpt 60
-c str/complex/step07a_npt.gro
-e bin/edr/step07a_npt.edr
-g run/log/mdlog/step07a_npt.log
-noappend
ERROR:
>
Fatal error:
Cannot change a simulation algorithm during a checkpoint restart. Perhaps you
should make a new .tpr with grompp -f new.mdp -t
bin/cpt/step06d_nvt_ann_LONG.cpt
_____________________________________________________________________________
Relevant answer
Answer
My understanding is that you produced a new binary (step07a_npt.tpr) from a new .mdp file (step07a_npt.mdp), and now you are trying to continue the previous nvt run (step06d_nvt.*0, right?
In that case this is wrong
$ gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr
-cpi bin/cpt/step06d_nvt_ann_LONG.cpt
-o bin/trj/step06d_nvt_ann_LONG.trr
-x bin/trj/step06d_nvt_ann_LONG.xtc
-cpo bin/cpt/step07a_npt.cpt -cpt 60
-c str/complex/step07a_npt.gro
-e bin/edr/step06d_nvt_ann_LONG.edr
-g run/log/mdlog/step06_nvt_ann_LONG.log
You are using a NEW mdp file, and generated a NEW binary. The info from the previous state should be already inside the new binary, that's why in the preprocessor phase you wrote the flags -c, -r, and -t. Therefore this
$ gmx_mpi mdrun -v -s bin/tpr/step07a_npt.tpr
should do the work. Consider that -o, -x etc specify the OUTPUT options, not the input, therefore when you write
-x bin/trj/step06d_nvt_ann_LONG.xtc
you are telling mdrun to write your trajectory to that file, not to take from that file and continue it. The error you get in the first case is related to the fact that the -cpi option is a continuation from a checkpoint, which is going to search for some files to continue a given run. This is useful when a simulation crashes or when you want to make a simulation longer. For example, you run 100ns of something and would like to go to 150ns. Then you run gmx conver-tpr, you extend the tpr file time and continue from there (using -cpi flag, read https://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html)
Here you got a new tpr, so you don't have to specify the -cpi flag.
Second error is similar. You are going from NVT to NpT, therefore you are now coupling the pressure. What mdrun is telling you is that it is not able to go on with the NVT phase because the tpr you are using (the step07) has something different from the state you are trying to continue (step06), most likely the barostat but something else as well for sure.
If you want to make the NVT longer you can go
gmx convert-tpr -s npt.tpr -extend TIME_YOU_WANT_TO_EXTEND_IN_PS
and then go
gmx mdrun -v -s npt.tpr -cpi npt.cpt
In this case you want a NpT, so a change in the binary, therefore you (rightly) compiled a new tpr (specifying the input status with -c/-r/-t flags) and can now just run the
gmx mdrun -v -s npt.tpr
Hope this is clear! :)
Nicola
  • asked a question related to Molecular Modeling
Question
4 answers
Hi,
I am a new user of ORCA. My initial calculations were successful but at this moment I am facing a problem to run a new calculation on my laptop. However, I can run calculation with the same input file on my older laptop.
Here is an example of my input file for the calculation on nitric oxide:
!RKS BP86 RI SV(P) SV/J TightSCF Opt
*xyz 0 2
N 0 0 0
O 0 0 1.2
*
Here is the error message mentioned at the bottom of the .out file:
ERROR : GSTEP Program returns an error
cannot continue with the optimization
COMMAND : orca_gstep NO.ginp.tmp
RETURN CODE : -1
I would appreciate your help.
Best regards,
Subrata
Relevant answer
Answer
This is due to the difference between the number of cores in the input and sbatch files.
  • asked a question related to Molecular Modeling
Question
3 answers
I am trying to create a similar diagram to this one attached below for my ligand. I ran a 100ns for the complex of ligand and protein. i am willing to consider interaction fractions of hydrophobic and h-bonds interactions only since my ligand is not charged, thus electrostatics are zeros.
now i was told i can calculate the nonbonding energy and vdw energy using the NAMDenergy plugin in vmd. so my files were in gromacs format. therefore, I converted them to dcd and psf by saving my trajectory in dcd format and using these two commands in vmd console to get the psf file
set all [atomselect top all]
$all writepsf XXXX.psf
unfortunately, i got this error from NAMDenergy plugin:
FATAL ERROR: Structure (psf) file is either in CHARMM format (with numbers for atoms types, the X-PLOR format using names is required) or the segment name field is empty.
when i checked the psf file it was already in xplor format and the segment name filed is there as well. so i don't know why it is giving me this error. here is a part of my psf file
PSF
1 !NTITLE
REMARKS VMD-generated NAMD/X-Plor PSF structure file
68834 !NATOM
1 1 GLU N N 0 14.007 0
2 1 GLU H1 H1 0 1.008 0
3 1 GLU H2 H2 0 1.008 0
4 1 GLU H3 H3 0 1.008 0
5 1 GLU CA CA 0 12.011 0
6 1 GLU HA HA 0 1.008 0
7 1 GLU CB CB 0 12.011 0
8 1 GLU HB1 HB1 0 1.008 0
9 1 GLU HB2 HB2 0 1.008 0
so the questions are:
1- how to solve this error so i can calculate the nonbonding and vdw energies
2- how to calculate the energy for hbonds so i can fractionate it as well
3- is there alternative way to calculate these energies or to create such graph?
thanks in advance
loay
Relevant answer
Answer
It should be possible to define groups of atoms (such as ligand, individual amino acid residues), store sums of all electrostatic and van der Waals interactions between groups of interest, and, after the simulation is finished, to calculate ensemble average. I would also plot the histograms to confirm that the distributions are normal.
  • asked a question related to Molecular Modeling
Question
2 answers
ArgusLab is a molecular modeling, graphics, and drug design program. Any tips or advice about this software? Any training guide or help manual about it?
Relevant answer
Answer
I agreed with Bojidarka B. Ivanova. After seeing your question, I have tried the software to perform some simple calculations. I found the results are not consistent and non-reliable.
  • asked a question related to Molecular Modeling
Question
3 answers
I want to model my system of fiber and matrix for my molecular dynamics simulation. What are the various Software available for modelling system?
Relevant answer
Answer
Hi,
there is large palete of MD software packages that can be used for your system. It depends if you want free software or you can buy one. Also depends if you want only the MD solver or also visualization capabilities.
Im familiar with following software packages:
GROMACS
- free
- widely used
BIOVIA Materials Studio
- not free
- user friendly
- with nice GUI
LAMMPS
- free
- widely used on clusters
Best regards,
Milan
  • asked a question related to Molecular Modeling
Question
5 answers
Hi,
In the previous questions I have successfully performed and analyzed the MD from two small molecules with Desmond/Maestro. However, I found that MD with Desmond cannot simulate the bond forming and breaking which is a crucial part in the design of our drug delivery system. MD can only gave me the simulation of weak forces.
To the best of limited my knowledge, I found two ways. 1. Reaxff reactive force field. 2. Quantum mechanics simulation (QM/MM).
I tried the Qsite (a tool of QM/MM in the maestro), but it did not gave out a trajectory file that can be visualized and analyze with MDanalysis. So, I turned to Reaxff. Now, I am trying to use Amber/Reaxff package to do the simulation. Right now, I faced some installation errors in Amber. I have sent the problem to the Amber mail list.
My main goal is to simulate the reaction between two molecules (the binding of the drug delivery agent and the target ligand) Both of them are small organic molecules.
My questions are:
1. How can I analyze and visualize the results (trajectory) from QM/MM?
2. After the simulation from the Amber/Reaxff, how can I analyze and visualize the results (trajectory)? I found some information stating that traditional MD viewer and analyzing tools cannot do the job. Can you suggest some software that I can dive into?
3. How to get the parameterization of the small organic molecules?
Is my approaches correct? Please, I really need your advices.
Thank you very much for your help!
Relevant answer
Answer
Shang-Wei Li : Your general approach of introducing QM into the simulations is correct. As you have noted, classical MD is not equipped to model the breaking and making of chemical bonds. You might also take a look at another approach that is described in the following reference:
Journal of Chemical Education • Vol. 83 No. 1 January 2006
They make use of a free program, "Molecular Workbench":
  • asked a question related to Molecular Modeling
Question
2 answers
Where the dim.exxxxx presented this as it content:
"cp: cannot stat 'DIMCAR' : No such file or directory - VASP"
Relevant answer
Answer
Thank you, Hadi Jabbar Alagealy I have already read through that resource but did not present a clear answer as to why the error message that I shared
  • asked a question related to Molecular Modeling
Question
7 answers
Hello.
which one have more hydrogenic bond,alpha helix or beta sheet?
iappreciate your comments.
Relevant answer
Answer
Here is the video on the topic that explains hydrogen bounding in Alpha helix https://youtu.be/wM06U0IAv5c
  • asked a question related to Molecular Modeling
Question
4 answers
I would like to study the apo form (lipid-free) of a protein that only has been crystallized with lipids. I want to explore if it is possible to generate with a molecular dynamic a reasonable structure, making subtraction of lipids in several steps until obtaining the apo form. Likewise, I don't know if, during the molecular dynamic trajectory, it is possible to disappear lipids. I am thinking of using programs like GROMACS, AMBER, etc.
Relevant answer
Answer
You need to remove lipid before MD simulation. You can not delete or add any atom/residue/molecule during and after MD simulation, as it will destroy your trajectory data.
  • asked a question related to Molecular Modeling
Question
4 answers
I want to start some chemical reaction calculations, but I need some basic reference to get started. Thank you in advance. Sincerely.
Relevant answer
Answer
When dealing with QM calculations on chemical reactions, one basic problem is thermochemistry. The evaluation of thermodynamic parameters allows a theoretical determination of enthalpy, free energy, and entropy variations associated with the reaction and hence reaction constant. If this is your goal, I suggest strongly this paper, available for Gaussian but whose concept can be easily generalised:
I hope this may be a good starting point (as it was for me!).
  • asked a question related to Molecular Modeling
Question
7 answers
My ligand has a quaternized pyridine ring in it's structure, but after editing, when I export it from AutoDock Tools as a .pdbqt file and open it in Discovery Studio Visualizer, the structure of my ligand changes and nitrogen appears to no longer be quaternized (a C=N double bond is lost, the +1 charge on the nitrogen is lost, there are now only 2 double bonds in the ring). The rest of the ligand stays as is, the problem appears to be happening only to the quaternized nitrogen. Is there a way to fix this from happening?
Relevant answer
Answer
Yes. The programs/subroutines that do the calculations do this based on the properties of the individual atoms, independent of the bond model. There is no localised +1 charge on the nitrogen, which you would have in the protonated nitrogen, but the lone electron pair of the nitrogen is part of the aromatic pi electron system.
  • asked a question related to Molecular Modeling
Question
6 answers
We know that the brain sends and directs meaningful messages to control the patient's cells.
as we know, The brain is affected by factors such as diseases And we know that the brain also controls other organs of the body.nevertheless,Damage to the CELLS is visible on eeg?
Is Cancer Effective In EEG?
Relevant answer
Answer
Stomach cancer is cancer that may affect any part of the stomach and extend to the esophagus or small intestine, and it causes the death of nearly one million people annually. It is more prevalent in Korea, Japan, England and South America. It is more prevalent among men than women. It is associated with eating too much salt, smoking, and also low intake of fruits and vegetables. Therefore, it is believed that its spread in countries such as Korea and Japan is due to the consumption of salted fish mainly by Koreans and Japanese, as well as the use of canned food and food preservatives. Mucosal colonization of H. pylori is believed to be the main risk factor in about 80% of stomach cancers
Stomach cancer is diagnosed through an endoscopic examination that allows a biopsy to be extracted from the affected tissue, and then analyzed to confirm the presence of a tumor. Dr. Riccardo Rosati, a specialist in gastroenterology at San Raffaele Hospital in Milan, says, "Before undergoing treatment, the patient needs to do a series of other ultrasound and other examinations to check the areas, glands and organs covered by the disease, in order to determine the degree of its progression.
As a researcher, I believe that stomach cancer cells do not send messages to the brain due to the lack of associated neurons
  • asked a question related to Molecular Modeling
Question
8 answers
Hello to All,
When converting a pdb. file (generated by Materials Studio) of polymer model(PE,PLA) into lammps data file by VMD topo tools, there's too many atom types in the output file(lammps data file). What could I do to reduce the atom types in lammps data file?
Relevant answer
Answer
You can also use the OpenBabel free software..It is easy to use. choose lmpdat for the output format.
  • asked a question related to Molecular Modeling
Question
3 answers
In Becke's B3LYP hybrid functional, Fock exchange is being mixed with Slater LSDA exchange (and then plus gradient correction), plus correlation expressions. But what LSDA exchange parametrization is used?
  • It appears to me that Becke in his DFT Thermochemistry I paper (J. Chem. Phys. 96, 2155 (1992)) uses the VWN parametrization, being the then modern alternative to the older Perdew-Zunger version.
  • Then in his Half-and-Half paper (J. Chem. Phys. 98, 1372 (1993)), he apparently switches to the then recent Perdew-Wang 1992 parametrization.
  • In his 3-parameter hybrid (DFT Thermochem III) paper (J. Chem. Phys. 98, 5648 (1993)) he seems to only comment on correlation being taken from the PW 1992 parametrization and not mention which LSDA version he uses for the exchange part, presumabely still the standard Slater exchange (E_X ~ int n_(alpha)^(4/3) + n_(beta)^(4/3) dr.
So which LSDA parametrization is used nowadays in B3LYP? Did people stick to the VWN version from Becke's initial paper or did they switch to the more modern PW version as Becke probably did? Or do different implementations in program packages use different versions?
Relevant answer
Answer
There are some references that might prove helpful:
Sholl. D.S. and Steckel, J.A., Density Functional Theory: A Practical Introduction, Wiley, 2009. Page 218.
Here some parameterizations are specifically mentioned.
(3) The Bretonnet article is attached.
I hope you may find something of these to be of use.
  • asked a question related to Molecular Modeling
Question
1 answer
How is the value for the spring constant (force/time units) and velocity (distance/time units) determined for any Steered Molecular Dynamics simulation? Is there an exact science behind it or is it more about referring previous published literature and using the values from there?
I am pretty new to both MD Simulations and SMD, so any insight is appreciated.
Relevant answer
Answer
I would say that it largely depends on what you want to do. For example, do you want to perturb the system or to drive a near-equilibrium transformation?
This being said, looking for previous works done in the same field is quite mandatory to see what has been done, what constants have been used and so on. If you want to unfold a protein, you will need to use force constants large enough to actually unfold it, and not play a tug-of-war with the intra-protein forces of the system. On the other hand, if you want to drag a solute/permeant through a membrane/a protein channel/a nanotube/etc. you may want to not perturb/disrupt the bilayer, or you may want to sample the interaction along the protein channel therefore you need slow velocities to let the permeant interact with its surroundings.
Overall, apart from the limits intrinsic to the software you are using and to the artifact you can introduce, it greatly depends on the theory you are applying. Does it depend on the velocity/k constants? Are you sampling states which need equilibrium conditions, and therefore must perturb the system the least possible? Or does it depend on fast dragging with ensembles of out-of-equilibium trajectories? Does it depend on any approximation, like stiff-spring which maybe would work better with constraints rather than restraints? Or maybe are you trying to reproduce a pulling AFM experiment, and therefore can get some insights from the experimental work?
In a way, it is always a matter of trial and error and checking was has already been done.
Hope this helps,
Nicola
  • asked a question related to Molecular Modeling
Question
5 answers
Hi,
I'm working on one of the ORC protein that is usually found in a complex for the most part of the cell cycle: from G1 to the end of S faze. But it is present in the nucleus as a single molecule in G2. It structure is available in the PBD repository but only in the complex. Is there any approach you can take to model a protein like that out of the context of the complex it usually resides in?
Relevant answer
Answer
Thank you both for your answers. I hope in time I will have an opportunity to help you in the future as much as you have helped me.
  • asked a question related to Molecular Modeling
Question
9 answers
I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands!
what I need is to connect them into one to run molecular dynamics simulation, what is the best tool to do so, also what are the steps to make sure that it will be mostly accurate?
Relevant answer
Answer
Try Ligandscout or Maestro, Schrodinger.
  • asked a question related to Molecular Modeling
Question
3 answers
I want to parameterize a few molecules. I need of course torsional, dihedral angles, charges , etc.
What is the most popular program for that right now? I know that gaussian is quite popular, but it is not for free. I want to parametrize lipids: mgdg and dgdg in OPLS-AA force field and some other molecules in charmm force field. I need also something which has quite good tutorials because I want to learn that things.
Relevant answer
Answer
You can also use GAMESS
  • asked a question related to Molecular Modeling
Question
6 answers
I am currently performing coarse-grained MD simulations in LAMMPS using mW potential for water. I initialize the water model at 273K, equilibrate for 50ns followed by a quenching process from 273K to 200K at a rate of 0.5K/ns for a total of 146ns. At the end I observe what looks like a nucleated structure. But how can I be certain that homogeneous nucleation has indeed taken place?
Can a specific property be extracted from LAMMPS or any visualization technique be used to confirm that the structure has indeed nucleated?
Any insight is appreciated.
Relevant answer
Write a script to calculate the radial distribution function of your system along a predefined reaction coordinate between the interface and the buried atoms. Check the coordination number and the behavior of the RDF to get insights about nucleation.
  • asked a question related to Molecular Modeling
Question
3 answers
I would like to perform a computational study of how solvatochromism is affected by viscosity of the medium.
I usually use Gaussian as software for molecular modelling, and my question is whether is it possible to include the viscosity in a Gaussian calculation for a UV-Vis spectrum or if there is a software that could do this.
Does anyone know of a software or approach that could help me with this study???
Thanks in advance
Relevant answer
Answer
This Question which interested me a lot, thank you very much
  • asked a question related to Molecular Modeling
Question
4 answers
If I have to draw a FCC 111 surface, am assuming the miller indices are: [1,0,0], [0,1,0] and [0,0,1]
How can miller indices be determined for orientations like FCC 211 or FCC 110 etc.?
I am trying to build atomic models through ASE Python, so any help in that regard will be greatly appreciated.
  • asked a question related to Molecular Modeling
Question
3 answers
I am trying to calculate the RMSF plots for some trajectories that have periodic boundary conditions. Unfortunately, I am unable to do this in GROMACS due to installation issues, so I have to use the Python-based MDanalysis instead. During my trajectories, the proteins do end up partially crossing the boundaries. Is there a way to calculate RMSF under these constraints? How might I do this?
  • asked a question related to Molecular Modeling
Question
3 answers
Dear colleagues, I have some experience with MD for studies of drug-target interactions, mainly NAMD and Amber. For quite some time, I wanted to try studying the binding/unbinding process of the drug to/from its target. I was thinking of using Steered MD, is it a good approach? I have seen some tutorials for SMD to “unbind” the ligand but none such tutorial to “bind” a potential ligand to its target. Is it even doable this way? Have you come across some tutorials for this?
What should I consider for such simulations, e.g. should the protein be restrained to limit its movement and inherently the SMD vector? should I use temp/pressure control?
Thank you for your responses.
Relevant answer
Answer
Starting with a ligand bound complex and probing the unbinding path should require no restrain, but if you start with a dissociated state, restrain is necessary. Otherwise, the ligand would possibly never find its binding site.
  • asked a question related to Molecular Modeling
Question
3 answers
Upon equilibrating an Ice Ih structure at 250K and using write_data command for obtaining the end structure post-equilibration, I found that it does not contain the required bond information that was present in the initial geometry file.
Also, if the previous bond info from the initial geometry file is copied over to this new post-equilibrated data file, the bonds look incorrect on visualization and LAMMPS gives an error stating "Inconsistent image flags" and "bond/angle/dihedral extent > half of periodic box length"
Does anyone know how to write or extract the bond info post-equilibration successfully in LAMMPS? Attached are the initial (1hx20.lmp) and equilibrated (data.equibicev2) files pertaining to the problem.
Any insight is appreciated.
Relevant answer
Answer
The LAMMPS trajectory does not contain the bond topology information. The psf file should be made on your initial configuration. If you are not using create and delete bond then pre and post equlibrated structure will sure find the correct topology from the psf file.
  • asked a question related to Molecular Modeling
Question
6 answers
Hi, I've been an experimentalist throughout my career and I want to add to my knowledge and expertise in Materials Science by delving into computation, modeling and simulation. However, I'm very confused about where to begin as it appears that field of modeling and simulation is quite vast and expansive. If I had to choose a starting material type, I'd say composites and modeling of failure modes of composites. Can anyone guide me on where to begin? I'm a complete novice when it comes to anything computational. Where do I begin, if I'm starting from scratch.
Relevant answer
Answer
  • asked a question related to Molecular Modeling
Question
4 answers
These concerns MD simulations using Gromacs. Suggestions involving Amber/LAMMPS/etc., aren't going to be of any help.
I'm looking for strategies that might save me on lines of code.
As I am sure you are aware there are several strategies for relaxing a protein in a bilayer. For example, a population approach is placing position restraints on the backbone which are decreased between simulations whilst preserving velocities. Finally, all position restraints are removed and the simulation is left to run unrestrained. This is useful for a sequential simulation->simulation->....->simulation, where the velocities are preserved.
My concern is when I want to run e.g., 4 identical simulations, each with different starting velocities. That way I can cover more phase space and I can calculate a metric of uncertainty when I'm measuring a property. This is very easy to do by hand. Each of the four production runs will use preserved velocities for a separate set of equilibration runs i.e.,
Sim1: eq_run -> eq_run -> eq_run -> production_run
Sim2: eq_run -> eq_run -> eq_run -> production_run
Sim3: eq_run -> eq_run -> eq_run -> production_run
Sim4: eq_run -> eq_run -> eq_run -> production_run
But this becomes very difficult when I have e.g., 100 models to build and run. That's 4*100 + 4*100 + 4*100 + 4*100 simulations with all corresponding files. Ultimately, I am looking for a strategy where I can introduce a bias or short external influence so that each model shares the same equilibration runs before spawning 4 unique production runs but without destroying the velocities preserved from the equilibration simulations i.e.,
Sim1,2,3,4: eq_run -> eq_run -> eq_run -> production_run1/2/3/4
I have a feeling, something like replica-exchange might work? Introducing 4 different temperature that gradually relaxes back to what they should be over a very short period of time just so that the preserved velocities diverge.
Thoughts are most welcome.
Relevant answer
Answer
The strategy you're trying to find is self contradicting. You try to "cover more phase space" by introducing some kind of perturbation from the same point in phase space (end of equ runs). But if you try to preserve the exact state at end of equ runs, it's limiting your exploration of the phase space.
If the only reason of asking this kind of strategy is file management, I'd suggest you to use scripts to do that. Trying to explore more phase space by starting from the same state point doesn't make sense, considering after the "perturbation", you still have to wait for your system to reach equilibrium again. It's equivalent to starting from, say different initial velocities.
Having said that, simulated annealing seems a good candidate of the "perturbation". Just raise/lower the temperature to some random temperature. Again, you have to wait the system to reach equilibrium after restoring your target temperature.
  • asked a question related to Molecular Modeling
Question
11 answers
Hi to all, I'have to perform a docking in haddock. i have determined the most susceptible residues upon ligand binding by chemical shift perturbation. now i need to determine which among the are active resiues, and i need to calculate which of them have a >=50% solvent accessibility.
I know that NACCESS is a very reliable program to do that, but i have to send a mail (a normal mail) to get the code for decrypt the rar file.
Is there anyone that could give me that code? or is there any software as reliable as NACCESS capable of perform that calculations?
Thank u
Relevant answer
Answer
You can use this very user friendly web server for ASA calculation http://cib.cf.ocha.ac.jp/bitool/ASA/
  • asked a question related to Molecular Modeling
Question
4 answers
Applications in Drug Design and Molecular Modeling
Relevant answer
Answer
RDKit is a popular Open-Source Cheminformatics Software.
  • asked a question related to Molecular Modeling
Question
4 answers
It is well known that for a closed shell (all electrons are paired up) molecule, the HOMO-LUMO gap is related to its stability. However, I often see that the same argument is used for open-shell systems (Unrestricted calculation). In such a case, the authors consider energies of both alpha and beta spin orbitals, and the orbital with the highest energy is considered as SOMO. Similarly, the LUMO is decided among both alpha and beta, and the respective gap is considered as the SOMO-LUMO gap. Next, the authors discuss the stability of the system based on that value.
However, to the best of my understanding, for an unrestricted calculation, three SOMO-LUMO gaps can be calculated (1) Gap between alpha spin HOMO and alpha spin LUMO (2) Gap between beta spin HOMO and beta spin LUMO, and (3). The method I mentioned above (considering both alpha and beta).
So, my questions are the following,
a) Is it technically correct to relate stability with the SOMO-LUMO gap calculated by method 3 for an open-shell system? Is it even possible to draw such a relation? How correct are such value and such correlation? If yes, then is there any reason why we are ignoring the other two gaps?
b) Are the gaps obtained by an unrestricted calculation have any practical significance at all (As argued here: https://joaquinbarroso.com/2018/09/27/the-homo-lumo-gap-in-open-shell-calculations-meaningful-or-meaningless/)
Any insightful response will be welcome. Thank you in advance.
Relevant answer
Answer
The precise role of UV exposure time in controlling the orbital transition energies, optical and electrical parameters of thermally vacuum evaporated Se 50 Te 50 thin film
  • asked a question related to Molecular Modeling
Question
5 answers
I am not sure whether crystalexplorer is corrupted or not? I have tried to open .cif file downloaded the Crystallography Open Database, but still can't open it ? I hereby attach this file and please do check it. if it works well, please advise how I can perform hirshfeld surface analysis?
Relevant answer
Answer
Probably the latest version does not match with the hardware of your system.
  • asked a question related to Molecular Modeling
Question
5 answers
I have a pre-equilibrated Ice 1h structure at 250K. I also have an Aluminium substrate which is 10 Angstroms below it within a simulation box. With the potential defined for structures (TIP4P for Ice, EAM for Al, LJ for cross-interactions), how can I bring both structures together to form an adhesive bond at the interface?
In terms of LAMMPS commands, how can this be achieved? Any insight is appreciated.
Relevant answer
Answer
Abhay Vincent in your model the LJ cross-interactions are the only ones between ice and Al, and the adhesion will be a consequence of them. Those are nonbonded pair interactions, so you don't need to create anything in terms of topology.
  • asked a question related to Molecular Modeling
Question
4 answers
Is it possible to transfer heat from one group to another using simulated aneeling technique in the Gromacs software? I would like to transfer heat from a gold nanoparticle (group 1 from 310 to 350 K) into a dppc bilayer (group 2) that is at 310 K. How can I do it using a NPT ensemble in a molecular dynamics?
Relevant answer
Maybe you have to apply a linear or non-linear temperature increments and decrements for each group. AMBER package can do it, but you can make a script for gromacs, perhaps it is already implemented in last version of gromacs, I dont know. Also, you can try with three groups: nanoparticle (group-1), polymers in the first and/or second shells (group-2) and remained polymers (group-3). Thus, you will only modify the temprature in group1 and group2.
  • asked a question related to Molecular Modeling
Question
6 answers
I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the said force field. So, how do I include an additional force field in GROMACS? Or, can I even use other force fields not included in the package?
Relevant answer
Answer
The easiest way to go is to actually prepare your system with Amber (as Glycam06 is in Amber format, as far as I know) and then use some converting tool to switch to gromacs, for example parmed
  • asked a question related to Molecular Modeling
Question
3 answers
I am a beginner and I found some tutorials on GROMACS website. Although I was able to follow some of steps through typing commands in ssh window, but I wasn't successful to run energy minimization step because I don't know how to write the script file specifying number of processors that can be utilized for running energy minimization. your help is really much appreciated.
Relevant answer
Answer
Here I hope you find this link helpful:
  • asked a question related to Molecular Modeling
Question
5 answers
Hi,
I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol to move the layer along the fibril axis to make the next layer, and then repeat this step to make other layers.
For example, to make a 4-layer fibril from the original fibril layer (chains D and J of PDB structure 2LMO), my commands are:
fetch 2lmo; hide all;
create layer1, chain D+J; translate [0.02, 0.25, 4.47], layer1, camera = 0;
create layer2, layer1; translate [0.02, 0.25, 4.47], layer2, camera = 0;
create layer3, layer2; translate [0.02, 0.25, 4.47], layer3, camera = 0;
create layer4, layer3; translate [0.02, 0.25, 4.47], layer4, camera = 0;
as cartoon, (chain D+J) + layer1 + layer2 + layer3
The result is shown in the attached PyMol session file.
From the Internet, I learned about the Iterate and Alter commands in PyMol, but they are intended for repeating an operation "on the atoms in a selection", not for repeating an operation "for multiple times". Therefore, I am wondering if there is a way to repeat the translation (or other operations in general) in PyMol by iteration or other methods. I need to construct a fibril structure of 10 - 20 layers and apply this method to different protein fibrils, so the automation of this process will help a lot.
Thank you for your help in advance!
Regards,
Gangtong
Relevant answer
Answer
You can use the programming language python from within pymol, which allows you to do loops. Either you write a separate python script "script.py" which you invoke with "run script.py" (https://pymolwiki.org/index.php/Python_Integration) or you embed a python segment within an ordinary pml script, e.g. just to make a loop by bracketing your python commands between "python" and "python end" commands.
Note that to call pymol commands from within python code, you need to use the pymol api format, e.g.
"cmd.translate(list vector, string selection = "all", int state = 0, int camera = 1, string object = None)"
instead of "translate vector [,selection [,state [,camera [,object ]]]]"
So you can make a loop that runs over a given number of iterations:
python for i in range(1, 25): ...
python end
  • asked a question related to Molecular Modeling
Question
4 answers
It is hypothesized that the nature/energies/electron distribution of the frontier orbitals of a molecule changes under external field condition. Under applied bias, the molecule can be oxidised/reduced and this changes its electronic distribution and eventually the molecules ability to conduct current. Can we model such an hypothesis using DFT in Turbomole? Some information in this regard is very welcome.
Relevant answer
Answer
Almost all quantum chemistry codes support applying external electric field in calculations. My recent work about ultrastrong regulation effect of electric field on various properties of cyclo[18]carbon is a typical example: https://doi.org/10.1002/cphc.202000903.
  • asked a question related to Molecular Modeling
Question
5 answers
Hi everyone. I used to be able to do this and I remember that it involved a command prompt based piece of software but I can't remember what it was. I have a folder full of .mol files (although I am struggling with that format so might change it) and I want to create a ligand database for screening using ArgusLab. Can someone tell me what the best option is for doing that?
Relevant answer
Answer
  • asked a question related to Molecular Modeling
Question
3 answers
Dear community,
As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data.
However, in many cases (e.g. attached image), when you visualize the densities, there are negative (red) density blobs not containing any atoms inside. Just empty space inside. There is nothing in the model in those regions of space. How it should be interpreted?
Could you tell me please what I am missing?
Would be grateful for any help,
Best wishes,
Aliaksei
Relevant answer
Answer
Even in a well-refined structure some residual difference density is always expected. In this case the small negative peak could have to do with imperfect bulk solvent modelling/scaling. I wouldn't worry about it too much, it's very minor in this case. The negative difference density at the carboxylic acid group of the glutamate however could be indicative of radiation damage; in that case refining with lower occupancy can be a solution. Other tell-tale signals for radiation damage are e.g. cleaved Cys-Cys disulfid bonds. HTH, Jonathan.
  • asked a question related to Molecular Modeling
Question
3 answers
First, I'm using VASP. It's known that surface defects can degrade desirable properties of some quantum dots. There's a molecule which is suspected to regenerate the dots by interacting with the defects. The QDs I'm interested in are cubical and around 20 nm, so I'm worried it'll be too many electrons for the cluster I'm on to handle. Should I:
1. Decrease dimensions to 1nm x 1nm x 1nm, place in a box with ~15 angstroms on all sides, and study the adsorptions from there?
2. Create a slab and study the adsorptions that way?
3. Do something else, possibly molecular dynamics.
I'm worried that the slab will fail to capture confinement effects, which may or may not be important for what I'm modeling. Similarly, I'm worried that going from 20 nm to 1 nm may be too far of a deviation from reality. What do more experienced modelers think?
Relevant answer
Answer
Before your study, you should check a slab size convergence of adsorption energy! Mohammad Saeed Bahramy wrote the right way to do it.
  • asked a question related to Molecular Modeling
Question
4 answers
I am trying to run an MD simulation of a protein in water using the OPLS-AA force field. I was supposed to assign the OPLS-AA standard charges to the protein atoms, but I got some issues with that. First of all, the energy minimization did not converge and after a few time steps (around 1000) during the NPT equilibration run, the simulation stopped working. Therefore, I set up an identical simulation only changing the charge assignment method, in particular, I calculated the protein atom charges via the QEq method. Now it seems that everything goes fine, namely, the EM converges and I manage to perform both the NPT equilibration and the NVT production run. So, my question is: what's wrong with the OPLS-AA standard charges? Is it reasonable to use the QEq method to calculate the atomic partial charges for proteins?
Further simulation details as follows:
  • Temperature: 298 K
  • Pressure: 1 atm
  • Time step: 1 fs
  • Berendsen barostat and thermostat
  • Box: 127.082 X 116.037 X 64.977 angstrom^3
  • 16 Cl- ions to neutralize the box (the protein has a net charge equal to 16 (e))
  • 30960 water molecules (TIP3P model)
  • Long-range cutoff radius: 7.5 angstrom
  • Neighbour list skin: 0.5 angstrom
  • Long-range method: SPME
  • Software: CULGI (commercial)
Relevant answer
Answer
Unfortunately, I am not using Gromacs to set up and to run my simulations but another commercial software as I wrote in my first message. I don't even know if I should see a relevant error about electrostatics with this software.
  • asked a question related to Molecular Modeling
Question
6 answers
I am looking for some tools for disulfide bonds prediction and energy/structure estimation. What I have: patch-clamp results of WT, single and double cysteine mutant of the ionotropic receptor that are indicating the possibility of the disulfide bond formation. In addition, there are some pdbs of the receptor structure available, importantly, they are in different functional (apo, resting etc.) states. Also, I prepared homology models of single and double cysteine mutants based on respective templates. I would like to somehow asses the impact of this double mutantion and probability of the bond formation and differences between given structures/homology models. By far I found MAESTROweb and Disulfide by Desing web servers that allow for estimation of the bond energies and probability of the bond formation at all. Of course, it would be best to use some MD to simulate WT/double CYS/double CYS with disulfide ff patch receptor systems and compare them, but I am looking for some less time consuming approaches. I there anything you would suggest? Could be something like mentioned webserves but I would be also interested in some robust and coarse molecular modeling approaches.
Relevant answer
Answer
  • asked a question related to Molecular Modeling
Question
2 answers
Hi all,
There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result.
This is concerning Raccoon(1) original, not Raccoon2. The original Raccoon allows your current workstation to perform VS, the new Raccoon2 does not it must be a cluster with PBS queue).
I have two questions:
1) I performed an active site prediction using AutoLigand. From the results I have a site of potential interest, "#Option 7" from a calculation performed with 400 points. When I now come to perform a drug VS on the receptor, how do I specify the location of the potential site on the receptor? I do not want VS to scan the whole surface, only the site I had identified earlier.
I have tried to generate a map file for the receptor target. This is done by loading the target into AutoDockTools, loading in the predicted target .pdb. Building a grid box around the predicted site. However, when I save the grid output as a .gpf file, Raccoon will not accept this map file for the receptor. I see the error:
Map file not found! The .fld map is missing. Select another directory.
(A) Which tool generates the .fld file? (B) Why aren't these generated automatically by ADT? (C) Why does the save .gpf file reference e.g., map.<xxx>_for_docking.A.map yet these files do not exist?
2) I'm running Raccoon(1) along with the latest of AutoDockTools, AutoDock and AutoDock tools. Within Raccoon(1), when I've specified Ligand(s), Receptor(s), Maps, and Docking (all are green), I come to execute "G E N E R A T E" and I'm faced with the error:
Impossible to calculate the cached maps here:
C:/Users/.........\maps
GIVING UP...
Any idea why?
Why is it impossible to calculate the cached maps? No explanation is offered, only the somewhat dire and very unhelpful statement "GIVING UP...".
3) If I select "at each job" for the map generation, I end up with a slightly different error:
Impossible to create the directory:
None
GIVING UP...
Again, not much information to go on. I suspect having seen a post back in 2013 that the problems in (2) and (3) are related to incorrect atom-types in the ligand when generating maps/
Relevant answer
Answer
Uttam Pal A few things I've figured out. AutoDockTools will not generate all the map files Raccoon expects. I need to add additional e.g., <xxx>.Br.map by hand even though the receptor does not contain that atom type.
But that aside, I'm still getting lots of problem. Please see this question to:
  • asked a question related to Molecular Modeling
Question
2 answers
Is it possible to transfer heat from one group to another using simulated aneeling technique in the Gromacs software? I would like to transfer heat from a gold nanoparticle (group 1 from 310 to 350 K) into a dppc bilayer (group 2) that is at 310 K. How can I do it using a NPT ensemble in a molecular dynamics?
Relevant answer
Answer
You can define gold nanoparticle and dppc bilayer as two individual temperature coupling groups, and set simulated annealing for group 1, but set tau-t of group 2 to -1 to avoid artificially maintain its temperature, you should be able to observe heat transfer phenomenon.
  • asked a question related to Molecular Modeling
Question
5 answers
After docking by Swiss dock server, I opened the target.pdb by chimera and then viewdock and then choosed DOCK 4,5 and 6 option. I could see the docking image and fitness values in a separate window, but I cannot locate RMSD values. can anyone please help? 
Relevant answer
Answer
Hi! I'm having the same problem! What did you do to visualize them?? I hope you remember it so many years later , lol. Thanks!!@
  • asked a question related to Molecular Modeling
Question
3 answers
Dear Researchers, I'm trying to simulate oxidation of SiC using LAMMPS. I need to add hydroxyl ( OH ) group to the surface atoms of SiC to prevent the fast reactions between oxygen and surface atoms (Si and Ca ). Anyone suggest a molecular modelling tool to perform this task.
Thanks
Relevant answer
Answer
Avogadro, Molden, Gabedit are some of the free molecular modelling softwares.
  • asked a question related to Molecular Modeling
Question
2 answers
I have installed the program in C drive and set this as C:\ligplot. This folder contains exe files and .cmd files of ligplot, ligonly, dimplot and dimonly. After installation I downloaded the example PDB 1A8A from RCSB. I kept this pdb file in pdb folder within ligplot folder. Then i started the ligplot command to execute the process as given in manual. There is one problem that says cannot find coordinate file. Can anybody help me in this regard. What is the problem?
Relevant answer
  • asked a question related to Molecular Modeling
Question
6 answers
Hi all,
Consider a circular plate's deformed configuration is available, and we know somehow the undeformed shape (perfectly flat with a defined radius). Is it a way to estimate average forces on the boundaries that resulted in the deformed shapes? Especially, is there a way to use off-the-shelf FEM packages like ANSYS for finding the average external forces?
A typical image of a deformed plate is attached.
Thanks
P.S. Pictures are from these two papers:
1. The pressure sensitivity of wrinkled B-doped nanocrystalline diamond membranes, S.Drijkoningen, S. D. Janssens, P. Pobedinskas, S. Koizumi, M. K. Van Bael & K. Haenen
2. Wrinkling membranes with compliant boundaries, Yuri Ebata and Alfred J. Crosby
Relevant answer
Answer
Ali Khalvandi Thanks for your suggestion. I'll try to read more about the method you suggested.
  • asked a question related to Molecular Modeling
Question
3 answers
I have a question.
I want to measure the volume per lipid. I built a membrane with water and run the simulation for 300 ns. To measure the volume per lipid I used a .gro file from the simulation and then run the lipid-free simulation with the same mdp parameters and check the volume of the box ( I just deleted all lipid from the system and run for example 50 ns and take the average volume of the box from 20-50 ns). So at the end my Volume per lipid = (Average (50-300 ns) box volume - Average (20-50ns) box volume from the free-lipid system) / number of lipids. Is that correct? I want to check POPC parameters fo so I will compare experimental value to those from my simulation
Relevant answer
Answer
Hi Jakub! If you are planning to use built-in routines in gromacs you shall use the one for energy (earlier versions g_energy, later versions gmx energy). As I understand, your bilayer contains the same lipid, which is POPC. So for the area per lipid you will need to extract the box sizes in xy-direction, multiply them by each other and then divide by the number of lipids in the leaflet. To obtain the volume per lipid you will need to determine the thickness of the membrane for each frame (if you plan to plot it per frame). The thickness can be determined from the calculation of electron density profiles or mass density profiles in z-direction. The distance between points of maximum of these profiles determines the bilayer thickness. If you divide it by 2, you will get a thickness of a leaflet. Then you multiply it by the area per lipid, you will get the volume per lipid. This is one of the simplest ways to do so. Some people also use Voronoi tessellation for computing the area per lipid, but since your bilayer contains only POPC, you can do it easier.
  • asked a question related to Molecular Modeling
Question
1 answer
Hello, I am interested in tracking the decrease in initiation events of different wildland fuel combustion.
Apart from the experimental procedures, is there any simulation software that can help me model the suppression of a burning object through water or water mixed with chemical additives?
Thank you in advance.
Relevant answer
Answer
I have mostly worked on accessing the combustion of coal and its causes through various sensors. However, CFD (computational fluid dynamics) have sufficient space for tracking the status of the fire.
  • asked a question related to Molecular Modeling
Question
3 answers
For the best of my knowledge, the absorption (excitation) energies calculations (using Gaussian) are performed on outer shell electrons therefore we obtain "simulated UV-Vis spectrum". But I need to calculate energies of core electrons so that I can obtain simulated X-ray spectrum. Anyone knows how to do that??????
Relevant answer
Answer
Thanks Ulf.......I need to calculate simulated X-ray absorption spectrum of benzimidazole derivative
  • asked a question related to Molecular Modeling
Question
12 answers
INVdock software has been used to predict the first receptor of drug with low molecular weight and finding or predicting cell target, I would be thankful to anybody who could let me know how could I get the software and procedure for working with the same.
How is the popularity of INVdock software?
is this software free and what is the procedure of working with that?
Relevant answer
After all that time, unfortunately, it still unaccessible.
Kindly see the attached file and the link below:
Regards
  • asked a question related to Molecular Modeling
Question
1 answer
Hi,
I'm trying to attach a carbonyl linker to Lys so that I can attach a PEG molecule to it. I have attempted so far by combining Lys , N-terminal and C-terminal topology data . But I'm having trouble deciding on the atom types I should use and the charges. Also whether I should stick to using CGENFF.
Linker and part of Lys topology file I have combined so far, ATOM CE CT2 -0.20 ATOM HE1 HA2 0.09 ATOM HE2 HA2 0.09 ATOM NE NH1 -0.70 ATOM HE HC 0.44 ATOM C C 0.51 ATOM O O -0.51
I have also attached my molecule below.
Any help would be appreciated,
Thank you
Relevant answer
Answer
Did you try this: http://www.swissparam.ch ("This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS."
Consult the answers to this question:
  • asked a question related to Molecular Modeling
Question
3 answers
In gromacs gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. then we use this S mol = 1/2(3cos^2 (θ ) − 1),.
So to compute the molecular order parameter for atom for example C3. We need to have indexes for atom C2 and C4 (because we write a vector and check the angle).
But what we should do, when we have the last atom in the tail. For example, I have oleic acid and I want to compute the order parameter for C18? How to do this? I can make an index for C17, but I haven't C19 (because this atom doesn't exist in oleic acid), so how can I write a vector? Maybe I should make an index for H atom at the end of the tail???
I ask you because I want to compare results from the simulation of my membrane POPC to these from 1 H– 13 C solid-
state nuclear magnetic resonance (NMR) spectroscopy and there they check C-H bond (so they don't use vector Ci-1 Ci+1 for Ci), so they are able to check this parameter for the last carbon of the tail.
And I also have a question.
why in NMR they use CH vector and then in GROMACS they use vector Ci-1 - Ci+1? And they have similar results I don't get it.
Thank you in advance for your help.
Relevant answer
Answer
Use the cpptraj tool in AMBER or some lib such as mdtraj for python.
  • asked a question related to Molecular Modeling
Question
5 answers
I am preparing the series of pyroxenes M1M2T2O6, changing the atom at T site. There are known pyroxenes with Li(Na)FeSi2O6, Ge can be as well at the T site. I would like to prepare Li(Na)FeSn2O6, but first I would like to model it and calculate the bond length and angle? Which program is the best for it?
Relevant answer
Answer
I know people who work on this line of research they use SIESTA code
  • asked a question related to Molecular Modeling
Question
3 answers
I am using Gromacs to analyze the interactions between protein-ligand.I am a beginner of Gromacs simulation. I have finished the simulation, I got the final gro , xtc, cpt, edr files, but not sure about how to do the data analysis. I read a research paper 'Characterization of the interaction of glycyrrhizin and glycyrrhetinicacid with bovine serum albumin by spectrophotometric-gradient flowinjection titration technique and molecular modeling simulations'. In this paper, they have done H-bond versus time graph and hydrophobic residue distance versus time graph, shown in attachment, to analyze the H-bond interactions and hydrophobic interactions between protein and ligand.
Does anyone know what command line can obtain these graphs and the steps?
Thanks a lot.
Relevant answer
Answer
  • asked a question related to Molecular Modeling
Question
5 answers
I created .prmtop topology and .inpcrd coordinate files in tleap, and then I ran minimization, heating, and equilibration steps, and then 10 ns of production with pmemd in AMBER 14 and created .rst and .mdcrd files for my protein-ligand complexes, I noticed when trying to view the trajectory in VMD, it looked like my complex went out of the box during some steps, and I just want to make sure I'm looking at the files correctly since I'm new to MD simulations. In VMD, I used the command "vmd complex.pdb", and then loaded the complex.prmtop file and then the complex.inpcrd file, and then the min.rst, heat.rst, and equil.rst files, and then the production.rst files for each of the 10 nanoseconds. Is this the correct way to view trajectories in VMD? What is the purpose of visualizing the trajectory for MD simulations?
When trying to load the files for one of my complexes in VMD, I noticed that my complex.inpcrd, min.rst, and equil.rst files jumped around on the screen into different positions, but after the prod.rst files, it stayed relatively in place. I also noticed that for some of my complexes, the RMSD didn't converge completely after 10 ns because there were very sharp sudden peaks in my RMSD graphs that I created with cpptraj, so I was wondering if the issue could just be my settings during the MD simulations, or if I'm selecting the wrong files to load into VMD. Should I load the .mdcrd files instead of .rst, or would there not be a difference?
Relevant answer
  • asked a question related to Molecular Modeling
Question
6 answers
I want to perform adsorption using DFT code but I can only create nanosheet like structure - supercells from primitive and use them to check their adsorbing selectivity towards certain gas.
I want to know if suppose a material, for example, Cr2O3 is selective towards a gas when I test it using DFT code (3x3x1 supercell of Cr2O3) and if I create nanoparticles or nanotube out of it, how will it affect its selectivity. I am aware nanoparticles will show more sensitivity which will be advantageous for me but I don't have any idea how to create one in my DFT software (I am using Quantum ESPRESSO).
Relevant answer
Answer
@yuvam bhateja, Sir, the effect of shape of the nano materials on sensitivity can be understood in terms of conduction path confinement, surface effect, etc. But there is no trivial answer for the effect of shapes on selectivity. Influence of crystal symmetry may have influence on selectivity( 10.3389/fchem.2019.00839). Selectivity towards a particular target gas increases if the specific adsorption towards that species is high. The indirect answer lies in understanding whether just by manipulating the shapes, can we change these specific adsorption towards a particular species. Shall keep you updated if I get an answer for you're question.
  • asked a question related to Molecular Modeling
Question
4 answers
What extensions/format should have those images?
Relevant answer
Answer
If you have a large screen, then a nicely zoomed pose can be used with keyboard print-screen screenshot with high resolution. I never needed to save or convert images in chimera.
  • asked a question related to Molecular Modeling
Question
6 answers
I am doing H-abstraction reaction by OH radicals. I found one TS, Which is barrierless. Is it possible. What  is reason behind it ?
Relevant answer
Answer
I would like to thank to Prof. Karaman for his explanation and the references.
We experienced several barierless TS in calculations of organic radicals binding weakly Br. radicals. In some cases this was apparently not due to thermochemical corrections (as reported in some references known to us) but due to an entropy penalty for some of the intermediates. We would like to understand the phenomenon (if not resulting from a method artifact) better, hence I am grateful for any hint.