Questions related to Molecular Modeling
Hello everybody !
I am working on a medium size organic molecule (around 40 atoms) and I try to check the presence of a conical intersection between S1 and S0. I used DFT and TD-DFT to compute the PES of S0 and S1 in my molecule along different modes and motions but for now no conical intersection was identified.
Do you think it would be a possible and interesting approach to use TD-DFT/MD simulation to start from the S1 optimized geometry and apply temperature to check the evolution of the geometry in the S1 state of the molecule in time ? Will it go back to the S0 optimized geometry in the case of an easy accessible conical intersection ?
Thank you for any help you may provide and for your interesting comments about it.
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.
Are you familiar with Research4Life? It's a program that provides free or low-cost access to scientific research in low-income countries. Research4Life has two eligibility lists: Group A and Group B. Group A includes countries with the lowest gross domestic product, lowest human development index, and other factors that indicate lower-income countries. As an immunoinformatics, Bioinformatics and Molecular Modelling researcher, I'm calling on researchers from Research4Life's Group A countries to join me in collaborative research efforts. By working together and utilizing the program's valuable resources, we can advance our research and make a difference in the world. Best of all, with this collaboration, it will be completely free. #Research4Life #immunoinformatics #bioinformatics #molecularmodelling #collaboration
I want to perform a MD simulation in LAMMPS for a water droplet impacting a rough Copper surface at an assigned velocity and then nucleate this droplet into ice.
I have made the droplet structure and the substrate surface individually using ATOMSK. I'm able to equilibrate the structures in LAMMPS individually as well - both at 250K which is the target temperature. However, the output from the two equilibration (droplet and copper substrate) yields two data files using the "write_data" command that need to be combined in order to obtain the final system.
My query is on what will be the best technique to merge these data files for a final equilibrated structure that can be used in LAMMPS. Any help or insight is appreciated.
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.
I would like to understand numerical hessian calculation in molecular modelling better.
If I estimate the (semi)numerical hessian, so either using the gradient or only the energies for the displaced molecule, I get the hessian matrix. After mass weighting, diagonalisation, taking the root and some unit conversion, I end up with frequencies. In case of imaginary ones, I have a not fully optimsed structure or transition state.
After implementing all this in own code, I ended up with sometimes having imaginary frequencies for structure being in a geometrical equilibrium.
vector = diag.eigenvalues().cwiseSqrt();
For smaller molecules, the results fit to the results obtained with another program (some differences due to numerical noise). For larger molecules, there are imaginary frequencies I don't understand.
I found an illustrating whitepaper at
. Why would the force constants be different if the molecule is centered and reorientated, if at all. Is there something else I have overlooked?
The WIP code is located at:
Thanks and best regards,
We can estimate the pore diameter for a high-resolution TEM image visually and easily. At the same time the DFT calculations are based on molecular modelling and takes into account direct interaction of adsorbate with the adsorbent surface. If both methods gave different results, which would be taken into consideration?
How can I download DESMOND for molecular dynamics analysis from the website: https://www.deshawresearch.com/downloads/download_desmond.cgi/ ?
I have already tried filling out the form and so far I can't access the download link or receive any link by email. Has anyone had the same problem?
I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to generate the initial atomic structure of the system. The "nanomaterial modeler" module in CHARMM-GUI comes in handy creating the atomic structure. But I do not have complete control over my structure if I use it. I need to attach the hydroxyl groups to the dangling silicon atoms in the interface as well. Therefore, it feels a bit complicated when defining the bonds and angles in the system using Matlab or python. As I'm using CHARMM potential, the relevant potential parameters need to be specified as well in the atomic data file. Any advice would be highly appreciated.
This is the system I could generate from CHARMM-GUI,
I want parameterise the ZN metal, which is coordinated with CCCH (three CYS and one HIS residues) residues. I just followed MCPB tutorial. While side chain modelling i got errors and unable to fix the problem. Here, i have attached my pdb file , sidechain.bcl file and sidechain.bcl log files.
I am trying to do simple modelling similar to the basic tutorial given on the modeller's website following error occurs while I compile in the same directory.
FATAL ERROR: Cannot open file build_profile.py: No such file or directory.
Please help me to figure out this.
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.
I am currently trying to make a solvent box with dichloromethane, which can then be used to solvate a solute I am working with.
For that, I embedded 1050 dichloromethane (DCM) molecules into a 5x5x5 nm box. The force field I am using is OPLS-AA. Energy minimization and NVT equilibration results look good. However, when I conduct the NPT equilibriation step, I run into the problem that the density of my dichloromethane box is given as 1.53 g/cm^3, which is quite far off the literature value of 1.33. I used the npt.mdp file from the well-known lysozyme tutorial (http://www.mdtutorials.com/gmx/), and ran it for a bit longer (1 ns), while changing the isothermal compressibility from 4.5e-5 (water) to 1.02e-4 bar^-1 (dichloromethane). I’ve attached the .mdp file.
Interestingly, when I look another DCM box (OPLS-UA forcefield) that has been made available through user contributions on the gromacs homepage (https://www.gromacs.org/user_contributions.html#:~:text=20%20May%202003-,ch2cl2_box.tgz,-The%20package%20contains), they used the isothermal compressibility value for water (!) and arrive at a dichloromethane density close to literature value. I did the same for my dichloromethane box and also arrive at a density of 1.34 g/cm^3, which is very close to literature. But surely there must be something wrong, with this, as I assume I can’t just swap compressibility values between compounds.
Is the higher density obtained with the dichloromethane compressibility much of an issue for further simulations? If so, what could be the problem with using the correct compressibility that causes the density to increase so much and is there a way to fix it?
I've attached the .mdp and files of my NVT equilibrated box.
Thank you all in advance! I appreciate any help with this issue, as I am fairly new in the field!
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?
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?
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.
Cannot find any complete set of parameters for Na-Al-Si-O (or sodium aluminosilicates) for ReaxFF. Any help will be very much appreciated.
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?
ValueError: Boost library location was not found!
Directories searched: conda env, /usr/local/include and /usr/include.
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.
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
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
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
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
-cpo bin/cpt/step07a_npt.cpt -cpt 60
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:
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
-cpo bin/cpt/step07a_npt.cpt -cpt 60
Cannot change a simulation algorithm during a checkpoint restart. Perhaps you
should make a new .tpr with grompp -f new.mdp -t
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.
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
REMARKS VMD-generated NAMD/X-Plor PSF structure file
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
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!
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.
I want to start some chemical reaction calculations, but I need some basic reference to get started. Thank you in advance. Sincerely.
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?
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?
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?
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?
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.
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?
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?
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.
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.
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
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.
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?
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.
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.
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.
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.
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?
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.
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?
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.
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?
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.
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!
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.
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?
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,
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?
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)
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.
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:
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:
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/