Re: [gmx-users] Software for PDB input for GROMACS

The nucleic acid builder should do what you want: http://structure.usc.edu/make-na/ Cheers Tom On 03/11/17 19:54, Dan Gil wrote: Hi, I would like to use the parmbsc1 force field to simulate DNA. I installed the force-field and am now actually running a simulation with a Drew Dickerson

[gmx-users] Software for PDB input for GROMACS

Hi, I would like to use the parmbsc1 force field to simulate DNA. I installed the force-field and am now actually running a simulation with a Drew Dickerson Dodecamer structure I downloaded from the RCSB database. Now I would like to generate my own structures and simulate them. I tried using

Re: [gmx-users] pdb (CTAB) into .GRO

One thing to try is to build the CTAB molecule with gmx x2top. You'll need to be careful about what it produces, but it can be helpful. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular

Re: [gmx-users] pdb (CTAB) into .GRO

Force field in gromacs reads only standard amino acids/DNA/RNA residue. In your pdb file residue name XXX is not defined in gromos ff. If your system is other than protein then use ATB to generate topolgy.

Re: [gmx-users] force field / parameters for NADH, FMN

Hey Justin, thanks - again -  for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]:   Overriding Bond parameters.   old:  0.1295 405848 0.1295 405848   new: CG2R64    NG2D1 1   0.1414   

Re: [gmx-users] angle/distance/position restraints in alchemical free energy calculation

On 11/3/17 9:36 AM, Wes Barnett wrote: On Fri, Nov 3, 2017 at 2:00 AM, minky son wrote: Dear gmx user, I’m studying about alchemical free energy calculation. I have been read some articles about restraints during free energy calculation, they referred the procedure in

Re: [gmx-users] angle/distance/position restraints in alchemical free energy calculation

On Fri, Nov 3, 2017 at 2:00 AM, minky son wrote: > Dear gmx user, > I’m studying about alchemical free energy calculation. > I have been read some articles about restraints during free energy > calculation, they referred the procedure in the article ( >

Re: [gmx-users] pdb (CTAB) into .GRO

On 11/3/17 4:49 AM, Adriano Santana Sanchez wrote: Dear all, I am a beginner with gromacs and I have already done some online tutorials. I am now trying to create from a PDB coordinate file (a CTAB molecule) the corresponding .GRO and .TOP files to run MD simulations. gmx pdb2gmx

Re: [gmx-users] force field / parameters for NADH, FMN

On 11/3/17 8:17 AM, Hermann, Johannes wrote: Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing

Re: [gmx-users] force field / parameters for NADH, FMN

Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing helped me a lot to figure out the few Nomenclature

[gmx-users] gmx wham problem

Hello I'm trying to obtain the PMF of an umbrella simulation using WHAM, but i get this error which i have no ideea how to solve : Command line:   gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal Note: Will use 8 OpenMP threads. Found 15 tpr and 15 pull force files in

Re: [gmx-users] pdb (CTAB) into .GRO

It seems that ctab.pdb contains residue 'XXX'. Verify that with pdb viewer such as pymol etc. Residue 'XXX' is not standard amino acid with 3 letter code so in lead to such error.Maybe you can delete it with same pdb viewer, or fix that naming error somehow. Its up to you to decide. On

[gmx-users] pdb (CTAB) into .GRO

Dear all, I am a beginner with gromacs and I have already done some online tutorials. I am now trying to create from a PDB coordinate file (a CTAB molecule) the corresponding .GRO and .TOP files to run MD simulations. gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce then choose

[gmx-users] walls and E-z

Hi all, It appears that the external field is refusing to move the ions when walls are present. I am comparing two setups of a system that has an aqueous bath (1M KCl) split by a semi-porous (infinitely selective for cations) membrane in XY. The only difference between them is that one is

[gmx-users] reliability of PMF

Hi, I've been trying to study a protein-ligand PMF using umbrella sampling strategy. So far, I have obtained the PMF following the tutorial and after performing bootstrapping the error is estimated to be at most 0.4 kcal/mol. Now, given the error value can I comment about changes like 2-3

[gmx-users] angle/distance/position restraints in alchemical free energy calculation

Dear gmx user, I’m studying about alchemical free energy calculation. I have been read some articles about restraints during free energy calculation, they referred the procedure in the article (http://pubs.acs.org/doi/pdf/10.1021/jp0217839). I tried to search mailing list, but still I couldn’t