Computational Biophysics - Science topic

Fatal error:

Group CNT referenced in the .mdp file was not found in the index file.

Group names must match either [moleculetype] names or custom index group

names, in which case you must supply an index file to the '-n' option

of grompp.

In my topol.top file, the [moleculetype] names is CNT, why did this error happen? What is the index file? 

I have attached the npt.mdp file. Can anybody help me?

Greetings,

I have a computational biophysics background and I want to enter the field of Deep Learning. How can I do this? should I read books, research papers, etc..?

I know how to program in Python and I have taken some online courses on Coursera about Deep Learning so I have some basics, however, the courses were general and not based on biology problems. Therefore, I want to start learning it again in a more scientific way to do my PhD in it.

What are your suggestions? and is it possible to self-learn it or do I need a supervisor?

Thanks

Hello all

Is there any reliable and free web server that runs molecular dynamics simulation of proteins?

When observing elastic modes of proteins, one of the results files shows deformation energy plot. What is the significance of deformation energy when studying protein dynamics?

Dear all,

I'm in principle a NAMD user but I'm new in performing MD simulation using polarizable force field. I wonder if anyone can suggest any MD software (NAMD or GROMACS, or ..) to implement polarizable force field easily and straight froward?

Thanks for your help,

All the best,

Zeynab

I am a little confused by the unit cell dimensions of the entry:

When I download the .pdb file there is only one molecule of protein with water accompanied by a unit cell dimension capable of fitting 4 molecules (this is viewed in the 3DView of PDB website as BioAssembly1). When I go to the link above and view in 3D, select "Unit Cell", it shows me 4 molecules of protein with water. 

I was hoping to find a way of downloading the 4 molecules to pack the unit cell, but I can't seem to find a way. Is there any way of recreating the packed unit cell in Gromacs i.e., replicated the protein molecule to create the 4 proteins in the correct position. 

While am running the EM, the minimizatin gets stopped before the forces get converged at step 14

Steepest Descents:

Tolerance (Fmax) = 1.00000e+03

Number of steps = 50000

Step= 14, Dmax= 1.2e-06 nm, Epot= 1.84916e+18 Fmax= inf, atom= 7809

Energy minimization has stopped, but the forces havenot converged to the

requested precision Fmax < 1000 (whichmay not be possible for your system).

It stoppedbecause the algorithm tried to make a new step whose sizewas too

small, or there was no change in the energy sincelast step. Either way, we

regard the minimization asconverged to within the available machine

precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not

needed for preparing to run moleculardynamics.

You might need to increase your constraint accuracy, or turn

off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.9#

Steepest Descents converged to machine precision in 15 steps,

but did not reach the requested Fmax < 1000.

Potential Energy = 1.8491607e+18

Maximum force = inf on atom 7809

Norm of force = inf

What should I do?

A number of post translational modifications can occur to a protein, including phosphorylation, methylation etc. I am aware that there are a number of servers and tools to predict positions for these modifications based on sequence and/or structural patterns or motifs. However, is there a tool (or server) available that can actually model them on a structure (or a model)?

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?

Dear all, 

I'm running simulations on membrane proteins (POPC) using Desmond software and I would like to use GROMACS tools to analyze certain parameters related to the membrane. Exemple:

- Deuterium order parameters of the acyl chains

- Density of the membrane environment

- Area per lipid headgroup

- Bilayer thickness

- Lateral diffusion of the lipids

Some files are easy to generate using VMD (.trr, .gro files) but I'm having difficulties to generate a tpr file.

Could you help me with any available tools please.

Thank you in advance for your help.

Zeineb

Few of us wanted to create a discord server for Biophysics. What we intend is to begin a commonplace for discussions/numerical experiments. Also possibly document the results in the form of blogs or other media.

I believe that there are many biophysics/computational biophysics/Molecular Dynamics enthusiasts here. Here is the server link: https://discord.gg/qRQRq2k

Come and join us. Let us learn together.

Hi All, I am trying to simulate one DMPG lipid bilayer in interaction with some fusion peptides. First I am preparing the membrane, and I am facing the problem: How to enable the NAMD to use NBFix parameters for SOD ions? Does anyone know how to set up this using NAMD and Charmm 36 FF?

Thanks in advance!

My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of any server /standalone programs for same?

I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by performing enhanced sampling MD studies, like Metadynamics, REMD etc., in which energy is added in particular co-ordinates called collective variables. This makes it slightly biased.

If I run unbiased atomistic molecular dynamics simulations of several microseconds, will my protein explore the conformational space by crossing the energy barriers? Or will the system be eternally stuck in a local minimum which it first reaches?

Hi!

So far I have been preparing my MD systems for NAMD using Modeller and CHARMM-GUI. I am thinking about switching to Schrodinger suite of programs. To perform MD I am using a supercomputing center not supporting Desmond. Is it possible to (without any complicated modifications) use systems (homology models with ligands, lipid memebranes etc) build in Maestro in NAMD?  

Hello!

For instance, in MD simulation of the the interaction between a peptide and a metal ion (like Zinc ion, Al ion, Mg ion etc.), does it possible to define the peptide as ligand and the metal ion as receptor?

Dear All,

I have an amino acid interacting weak with a CNT. During the standard MD it adsorbs, desorbs and then re-adsorbs on the CNT surface. Which method does suits to calculate the adsorption energy? Is there any fast and easy way to calculate the adsorption energy?

Thanks in advance,

Zeynab

Rather basic question for the experts. I have frames from 1.gro, 2.gro .....20.gro in order. I want to join them to a .trr or .xtc file to make a trajectory. How can i do it using gromacs commands. Thanks in advance 

Linear interaction energy

===================

How to define energy groups in protein ligand complex (solvated in water) and ligand in water?

Hi All,

I want to perform Molecular Dynamics (MD) simulation (using NAMD and CHARMM force field) of carbon nanotube/graphene with topological defect like Stone-wales. Creating topological defects changes the distance among carbon atoms from those using in pristine nanotube/graphene. I wonder whether I have to change the parameters like equilibrium distance and the spring constant value in the topology file or it isn't needed?

Dear all,

I want to run the molecular dynamics simulation of an infinite graphene sheet solvated in water using NAMD code. I don't know how to create an infinite sheet with it's periodic images. Should I add bonds between graphene and it's periodic images or is not needed?

Would be so much thankful to help me..

All the Best,

Zeynab

Dear all,

I have performed MD simulation for different carbon nanotubes (CNTs) in water using NAMD software. Each CNT is solvated in a water box initially and MD is performed for each box. Is there any way to quantify which CNT is better soluble? for example calculating heat of solution? If so, how I can calculate it?

Thanks every body ..

Hi All, I started simulation of reverse micelles in gromacs. After simulation I tried to visualise my system in VMD (it look like fig min.RM.png), to visualise properly I tried trjconv tool in gromacs but unable to relocate with in box. So I check with starting system, my initial system are not in the  center to box (see fig: pack.png)

Is there any way to visualise my system

Thanks

I was trying to simulate a 512-DPPC membrane after developing it from Tieleman's model of 128-DPPC bilayer. I removed the initial periodicity and the water molecules using trjconv as suggested by Justin Lemkul in his tutorial of membrane protein simulation (KALP15 in DPPC probably). I used genconf to place the 128-DPPC membrane sidewise in a 2(x) 2(y) 1(z) format.

The first picture i.e. of nice bilayer is after energy minimization using a steepest descent algorithm with a gradient of 100 kJ/mol/nm. It is only after NVT equilibration with a high position restraint applied on the DPPC residues, it is making a hole inside the membrane i.e. the bilayers tear apart.

I tried this several times changing the temperature (to change the membrane fluidity) and the gradient too (I primarily used 500 kJ/mol/nm and then reduced it to 100).

Any idea on how it can be solved? I see quite a few water molecules inside the bilayers which go out during equilibration. Also, the ions show a tendency to make a cluster at one corner of the membrane.

Please help...

I want to predict the protonation states of Histidine in my protein and I don't have any ligand. As long as I try Propka 3 (only protein) and Propka 3.1 (protein and ligand), I receive different results and I'm wondering which one is trustworthy. Can anybody help? Thanks.

I'm trying to study my protein in different pH conditions (using Gromacs) but how can I change the protonation state of some residues of my protein to mimic different pH? I have already used H++ but cannot proceed.

Hi Everybody,

Wish somebody help me to understand the following situation: Consider the MD simulation of two interacting molecule (first one on the left and the second one on the right) in a unit cell: The second molecule is interacting with the right side of the first one. Then, the second molecule start to get far from the first one and to get out of the unit cell, lets say the right-hand face of unit cell. Under the PBCs it has to enter from the the left-hand face and it interacts with the first molecule from the left side of the first molecule, while before getting out the cell it was interacting with the right side of the first molecule. I wonder if such simulation is correct...? I mean before getting out of cell the second one was interacting with the first one from its left side and if it interfaces the cell wall, it interact with the first molecule from its right side. There is a jump and I don't know how to deal with that during the simulation..  

I am simulating Protein-ligand interaction using gromacs and now I am getting this problem. Please held how to fix it.

Fatal error:

Too many LINCS warnings (1001)

If you know what you are doing you can adjust the lincs warning threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,

but normally it is better to fix the problem

Welcome for your assistance.. my md.mdp file is attached

I am trying to simulate do a Umbrella sampling simulation in GROMACS. I have the starting structure from XRD. The ligand sits almost at the middle of the lipid bilayer. I want to generate the initial  configuration for performing US. I am stuck with what I should give as the reference so that the ligand traverses from the extracellular side to the intracellular side. 

The values of the dipole moments of the given purine tautomers contain in the range of 1 to 23 Debye. I've got also Hirshfeld partial charges.

Hello all,

I would like to know how replica exchange umbrella sampling methods works , and how can i start by using plumed plugin to gromacs.

Thanks in advance,

Sincerely,

ANJI BABU

Hi everyone, I have a query to ask regarding molecular dynamic simulation by using Gromacs. When the running simulation was accidentally stopped, and re-run, should I need to type any command to combine the .gro file or any file?

Actually, I had run some simulation. The problem was, some of the graphs gave only 30ns (or less than 50ns) while, I am running for 50ns Md simulation. I have checked the .log file and found that the simulation was finished running for 50ns. Here, I attached the rmsd picture and the .log file for your reference.

Thank you.

i have done docking study using Patchdock and firedock of protein (pdb id 3F7Z ) with  ligand (gymnemic acid ) i got the result Global Energy - 62.74 ,( in autodock4 gave  -5.2 ).

when i am doing for the molecular stimulation with NAMD it shows

ERROR: Constraint failure in RATTLE algorithm for atom 848!

ERROR: Constraint failure; simulation has become unstable.

is it possible after getting good binding energy in docking then molecular simulation  become unstable ?

(Note: i have done with other protein (like PDB id :1c83, 1IRK ) with same ligand  i got good results  for molecular simulation ) 

I used gromacs to perform a 10 ns equilibration of POPC membrane. I've heard that we can use gmx density to get the bilayer thickness. I would be very grateful if anyone can suggest me how to use it to measure bilayer thickness. Thanks

I am simulating Aβ peptide (2BEG) with inhibitor, how to add molecules at random position prior to solvation, which was done by lemkul in his study.

Removed Question as account inactive and questions cannot be deleted

I am simulating Aβ Protofibrils (2BEG), I want to cap N terminal, How to cap it, I acetylat  N-terminal in pymol, and pdb was edited for CH3 to CA and run pdb2gmx following fatal error given.

  Fatal error:

Atom CD1 is used in an interaction of type atom in the topology

database, but an atom of that name was not found in residue

number 5.

I am trying to do protein folding studies for approx 70aa length protein using Gromacs. However, when I perform simulations, my protein goes out of the box and interacts with its images when simulated at 1.00nm box.

Can anyone please guide me as to how to calculate (if there is a formula or so) how big the PBC box should be such that no interactions are allowed between the periodic images?

i want to study the nature of protein dna interaction using charmm36, I face problem to generate the psf file of protein dna complex.

Dear all,

I am doing QM/MM study of protein. Earlier, I have done solvation and equilibration by using CHARMM22 force field in NAMD and input file for QM/MM in Gussian 09. So, my question is that can I use AMBER force field in NAMD? And if yes then what is the step by step description for solvating and equilibration of protein structure?

 

Hi everybody,

I would like to pull a ligand in a channel from my protein and calculate the PMF with Umbrella sampling. This channel is probably not linear and thus have to be refined. Too much colisions appears along a simple one axis pulling and causing a catastrophic PMF calculation.

Currently I'm working with Gromacs and I wondered if it is possible to define statically or dynamically the coordinates for the center of the channel and use it during the simulation (Pulling).

One solution could be to define in the md_pull.mdp configuration file all the transition points of my pathway through which my ligand must pass from my APO structure determined with CAVER.

Instantiation of Gromacs parameters of md_pull.mdp is not enough clear for me and PLUMED is may be a more direct solution. Currently I have no experience with PLUMED but It seems on paper to be able.

An other choice would be to define dynamically the channel center, on-the-fly. PLUMED seems also capable to manage this sort of challenge but once again I have no idea of the feasibility of a such work.

What do you think about this problem and of the tracks evoked above ? 

Cheers, FR.

Hello

    For learning purposes, I'm working on a simulation where the user can input any force equation and the application will apply that equation to all bodies on the simulation.

    For non-bonded atoms, I'm using Lennard-jones, but what should I use for the bonded atoms.

    For example. If I want to simulate a water molecule, I guess I should use the Lennard-jones for the H-H inside the same molecule, but which equation should I use for the O-H.

   Thank you -)

Dear all,

I am simulating a protein in solution, GROMACS 5.1, Verlet cut-off scheme.

I realised I put wrong charge groups in the topology file. I have read that with Verlet they are not considered but as a safety check I recompiled a tpr with the correct topology and run two simulation, from the same cpt file of an old one: one simulation continuing with the wrong set up, one with the correct.

The output is not identical (I run them on the same computer), but I am wondering if it is because of the charge groups or because with the new tpr I am introducing new sources of randomness. Can you help me? Or suggest a check to understand whether the charge groups are influencing the dynamics or not?

[in the tpr, original and new, gen_vel=no, continuation=yes, ld_seed=10 (same value)]

Many thanks

Hi,

I want to know whether the flat-bottom position restraints can be applied only for the pull code in umbrella sampling or it can be use for NPT or MD simulation of GROMACS (not umbrella sampling), If yes, please guide me how to use.

Regards,

Swati

I had run MD simulation with NAMD and want to check the differences of R of G during the simulation time. Is it important and efficient to record R of G? or there is another parameter that I should calculate?

Thanks

Abdo

SASA is the surface area of a biomolecule that is accessible to a solvent. If I define the amino acids forming binding cavity and measure the area of the surface, can that be considered as the total area available in that cavity or the area available for the inhibitor molecule...??

If yes, then can it be used to screen the inhibitors based on their total or topological polar surface area (TPSA)..??

I have seen many papers on folding and unfolding of peptides using Replica exchange with solute tempering (REST). How do we implement this method in GROMACS > 5.1?

Molecular Dynamic (MD) simulation is an effective tool to determine the movement of molecules and hence to predict the properties of suspension at interface.

I am facing problem to 1. generate code for the sample material, 2. Force analysis at interface.

Dear All,

I have tested with two ways of solvating a peptide with urea-water mixture in Gromacs.

Method 1: Pre-equilibrating a urea-water box and solvating the peptide with -cs option with this box

Method 2: Adding urea molecules to peptide box using -ci option and then solvating the resulting box with water molecules

In both the methods, same number of urea and water molecules were added . 10ns equilibration followed by 20ns simulation steps were carried out.

On analysing the properties, average number of hydrogen bonds between peptide-water in method 1 was 16.221 while it changed to 14.340 in Method 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to 4.031 on switching from Method 1 to Method 2.

On checking radial distribution functions, interaction between water-peptide sites were somewhat similar for both Methods but significant changes were found for peptide-urea site-site correlations. Method-1 showed higher peptide-urea interaction.

What could be the reason for these discrepancies? Are both methods correct?

I want to go on with Method-2 for further simulations because it is relatively simpler but Method-1 shows higher hydrogen bonding between sites.

Please suggest.

yours sincerely,

Apramita

I am working in the field of protein chemistry.  Can anybody help me to do molecular dynamics and simulation.Is there any institute who can help me to do so????

Hi

I would like to get he recent amber force field (topolgy-parameter) for performing MD simulations of RNAs containing modified residues. More importantly how to simulate system containing Guanine in Tautomeric form (force field)?

The H-bond graph between protein and ligand obtained after md is showing temporary bonds i.e. bonds are forming at certain frame and there is no bond at the rest of the trajectory. Please comment on this kind of ligand behavior. Also, is the interaction between ligand and protein is temporary in this case? What else can be done in order to assess the interactions after md.

Hi,

I am new to GROMACS. I have a doubt. Suppose I have two groups in my system and I  want to restrain the Centre of mass of a particular group, then how to specify this in the refcoord-scaling=com option, where to specify center of mass of which particular group it will consider for restrain.

Please give suggestions.

Hello, everyone!

    Now I'm studying on the MD simulation of interface diffusion. After I got the trajectory of the atoms, I didn't find the solution to obtain the atoms' RMSD along the z direction(vertical to the interface). The software I used is VMD. I want to know if there're some skill to deal with the problem.

Thanks a lot

what are the means and differences of "< |M|\S2\N >" , "< |M| >\S2\N" , "< |M|\S2\N > - < |M| >\S2\N" and "< |M| >\S2\N / < |M|\S2\N >" in .xvg file of g-dipoles command of gromacs?

I want to perform the brownian dynamics of graphene oxide using Gromacs, but I don't know what to do. I have done many molecular dynamics simulation of graphene oxide and I am familiar with the  procedures. In brownian dynamics, do I need to build the model of graphene oxide?  Is perform brownian dynamics same as perform molecular dynamics? 

Hi,

I want to perform molecular dynamics simulation of protein-RNA complex at deifferent pH condition in gromacs. 

When I am using Amber force field, It is not detecting protonated residues while OPLSaa force field is not detecting nucleotides. 

Is there any other software available to perform this simulation??

 I am using this command in cpptraj

rms ToFirst :1-81&!@CA,C,N,O*= first out rmsd1.agr mass

Plot is generate using  number of frames.How to plot rmsd of amber trajectories in time unit  ns using cpptraj ?

Hi,

I'm doing MD simulation using Amber. Every time when I measure the RMSF and RMSF it is always very high. I don't know what is the problem. THe RMSD remains stable but get high as 6 to 10 Angstrom. is this a problem or not. I also extend my simulation but no fruitful results till now.

I have also attached an RMSD plot for reference. 

Is polarizable MARTINI models compatible with atomistic models of protein (hybrid simulation) in NAMD? what considerations should I take for timestep in these cases? I'd appreciate your suggestions and comments with references to topo and par files. Is there a better or coarser model for water that can be used in NAMD? The simulation is aimed at docking analysis.

Hi guys, I am an undergrad who just started working on molecular simulations. Currently I have to do a molecular simulation with adenosine deaminase and guanine deaminase. PDB file of adenosine deaminase shows it contains a selenomethionine and pdb of guanine deaminase shows it contain a xanthosine. Those two residues cannot be recognized by amber or charms forcefields. What will be the best tool for me to create forcefield files for those two residues?

Hello everyone

I want to simulate a small organic molecule in which Iodine atom is linked to Carbon of benzene ring. I am using GROMOS54A7 force field and obtained atom types and charges etc. from ATB server. I am curious about the parameters for Iodine atom. Can I replace the atom name of I with C? Keeping the charges and weight of Iodine intact. And how to obtain the bonded and non-bonded interactions

Can someone suggest what "Molecular Dynamic simulation" is and how to study it? 

Hello,

I performed 20ns simulation of a protein using Gromacs 5.1. I want to plot  DSSP plot of simulated protein for specific residues. I created index file using following command. 

gmx make_ndx -f f.gro -o A.ndx

But when i used the above ndx file in DSSP command. I dont see desired residues secondary structure plot.

Can anybody please let me know how to do it.

Thanks,

Sai

Can someone suggest what "Molecular Dynamic simulation" is and how to study it? 

Schrödinger software

for a beginer

hello,

A protein which is composed of dimer of heteromers (αβγ). I want to simulate this protein to study the correlation between structure and function. what you will suggest for simulation to take the monomer form or in the form of dimer? is the monomer form simulation will represent their natural dimmer form?

Do I need to minimize my ligand using sander if I just wanna do standard molecular docking using AutoDock, not molecular dynamics? Do I have to stop until adding AM1-BCC charges by antechamber?

If no, what are the steps needed for ligand minimization after drawing it on MarvinSketch. Thank you.

Hello everyone,

Actually I faced a problem regarding movie making and analysis after simulation from multiple DCD file on NAMD.

So, actually I want to run 1000000 steps of steered molecular dynamics of a large protein containing 546445 atoms. so it was very much time consuming job. so i want to carry out the job using multiple restart file on NAMD.

But i don't know how to make the movie and final analysis of  the steered molecular dynamics job from multiple DCD file and Restart file.

So, can anyone help me to find out the solution.

Thanks in advance.

Hi everyone, I am using gromacs 5.1 for COM pulling of the ligand from a lignad-protein complex. I am getting an abrupt fluctuation in the position of the ligand near 110ns and 270 ns (as you can see in the attached figure) which should not be there. So my question is, What is the possible reason that leads to fluctuation and how it can be fixed?

I am trying to set up a molecular dynamics (GROMACS) simulation to study the effect of crowding agent on protein structure. I have referred several literature papers where they have mentioned modelling the crowding agent as a hard-core sphere but couldn't find relevant information to include spheres in the solvent. Can somebody please explain how to model and incorporate hard core spheres into the box along with the solvent and protein? Kindly let me know if any materials are available related to this work.

I am doing all-atom MD simulations. I want to simulate a complex system containing DNA and protein. I found papers, where most people have used AMBER force field for DNA/RNA systems. Earlier, I have done simulations with CHARMM36 forcefield for only protein system. I would like to know, whether should I continue with CHARMM, which also has the definitions for nucleotides or switch to AMBER forcefield for DNA-Protein complex and why?  

I would also like to know that what parameters in *.mdp change on changing molecule type (only protein to DNA/protein-DNA complex) and/or forcefields.

I am working on nucleic acid (NA). I have to add K(+) ions to study its behaviour. I want to keep the coordinates of NA molecule and K(+) fixed & allow water molecules to equilibrate. This step is necessary to prevent the fast diffusion of bare K(+) ions, unprotected by their solvation shells, towards NA. I want to carry out the following steps. 1) NA and K(+) fixed, water molecules are allowed to move (equilibrate) 2) NA fixed, K(+) and water equilibration 3) All three are free to move. I have generated the position restrain file (*.itp format) for K(+) by using .ndx file & genrestr command. My question is where and, how do I need to plug .itp file in topol.top.

Format of position restrain for K(+) is :

[ position_restraints ] ;

i funct fcx fcy fcz

141985 1 1000 1000 1000

141986 1 1000 1000 1000 : : here 141985 is the atom index of the first K(+) ion and so on.

I am simulating a single chain with AMBER force field. After energy minimization, I got a force less than 10 kJ/mol/nm, but energy converged to a positive value. Does it mean my simulation was wrong or something else?

Thanks in advance.

Jing