Re: [gmx-users] (no subject)

I think the answer is not so straightforward. It depends upon a lot of things, but I would say that the parameters derived using QM is better. If you do not have any other options you can still use PRODRG server but even in that case, I find many people using the docked (or bound) conformation of t

[gmx-users] (no subject)

Hii I am new to simulations. I want to ask is it ok to use ligand topology build using PRODRG server if using amber force field for RNA-ligand simulation. what precautions one should take ends of the RNA molecule. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

[gmx-users] "comm-mode = Angular" gives error

Dear Users, I am trying to perform simulation of a very large and complex system and which requires me to make the simulation box rectangular cube instead (box dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to minimize the number of atoms present in the system. I am facing the p

Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

Hello Bratin Kumar Das， Your answer is correst but irrelevent to my question. By adding energygrps option in the mdp and rerun the trajectory and generate the edr file containing the interation energy information which can be extracted by enemat. However enemat only gives the range of the inter

Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

You need to prepare one .mdp file where the energygrps = DNA Protein ( as example). Generate the .tpr file and rerun using mdrun module. gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc On Mon 19 Aug, 2019, 8:09 AM sunyeping, wrote: > Dear all, > > I am doing protein-DNA complex simulation

[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

Dear all, I am doing protein-DNA complex simulations with gromacs and I have gotten a trajectory. Now I want to calculate interaction energy between the protein and the DNA in every frame of the trajectory so that I can pick out a frame in which the interaction energy between them is the larg

Re: [gmx-users] Error Report

On 8/18/19 2:06 PM, Dr Adekunle Rowaiye wrote: Hello all, I need help. I got this while doing simulation. What do I do? File input/output error: protein_pr.gro This means that either (1) if this is an input file, it simply is not in the working directory or (2) if this is an output file, you

Re: [gmx-users] Not all snapshots are written to trr during minimization

Den 2019-08-18 kl. 17:10, skrev Dawid das: Dear All, I noticed that after my minimization run I have less snapshots in trr than I expected. For instance, the structure is written every 126-127 steps (plus the last one) even though my mdp file states nstxout = 100 Best wishes, Dawid Gra

[gmx-users] Error Report

Hello all, I need help. I got this while doing simulation. What do I do? File input/output error: protein_pr.gro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Su

[gmx-users] Not all snapshots are written to trr during minimization

Dear All, I noticed that after my minimization run I have less snapshots in trr than I expected. For instance, the structure is written every 126-127 steps (plus the last one) even though my mdp file states nstxout = 100 Best wishes, Dawid Grabarek -- Gromacs Users mailing list * Pleas

Re: [gmx-users] Topolgen

On 8/18/19 8:44 AM, Bratin Kumar Das wrote: You can use mktop for that...otherwise acpype is also a good option Indeed - TopolGen makes no effort whatsoever to actually parametrize a molecule. It uses known functional groups to try to assign atom types and charges. It relies on known speci

Re: [gmx-users] Wham analysis

On 8/18/19 5:10 AM, Negar Parvizi wrote: Dear all, I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is i

Re: [gmx-users] question on ffG43a1p force field

On 8/18/19 3:24 AM, Lei Qian wrote: Could I ask one more question about your *gromos43a1p.ff* force filed ? Thanks! I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce It shows a fatal error: "Fatal error: The residues in the chain xxx--xxx do not have a consistent type. The f

Re: [gmx-users] Topolgen

You can use mktop for that...otherwise acpype is also a good option On Sun 18 Aug, 2019, 1:32 PM rakesh parida, wrote: > Dear Team, > I am new to gromacs software. I have been generating the topology file for > the PF6(anion) by using topolgen1.1 software (with the Perl program). The > software

[gmx-users] Wham analysis

Dear all, I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex. The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for wham

[gmx-users] Topolgen

Dear Team, I am new to gromacs software. I have been generating the topology file for the PF6(anion) by using topolgen1.1 software (with the Perl program). The software is generating the skeletal of the .itp file for PF(anion) but there is no bonded parameter in that file. Please suggest me how to

Re: [gmx-users] question on ffG43a1p force field

Could I ask one more question about your *gromos43a1p.ff* force filed ? Thanks! I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce It shows a fatal error: "Fatal error: The residues in the chain xxx--xxx do not have a consistent type. The first residue has type 'Protein', while re