[gmx-users] mktop

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 13 02:51:25 CEST 2011

ram bio wrote:
> Dear Justin,
> Thanks, and I accept your suggestions;
> If SwissParam was designed to be used with CHARMM, the most intuitive 
> next step is to use CHARMM for the MD, is it not?I understand the point 
> about trying to keep the force fields consistent between docking and MD, 
> but it may not be feasible (i.e., there may not be suitable parameters 
> in OPLS for the bizarre functional groups you're dealing with).
> Yes, I also tried CHARMM FF to generate the topology file of the protein 
> using pdb2gmx (without ligand), and as per the swissparam and gromacs 
> tutorial i could build the protein-ligand-lipid bilayer and minimize it 
> using mdrun and and i am at the NPT equilibration step, everything is ok 
> with this procedure and without errors, but my lipid bilayer is made up 
> of POPC and the POPC itp file has OPLS FF topologies. So, i was 
> wondering whether the POPC itp file i am using for MD simulations can be 
> used with the protein and ligand topology file generated by CHARMM.

You shouldn't mix and match force fields.  Suitable CHARMM lipid parameters are 
widely available.

> and as per the swissparam tutorial the command to generate topology file 
> for protein is:
>  pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp
> in the gromacs 4.5.4 version the option to select Charmm FF from the 
> pdb2gmx command is available, but i could not understand the usage of 
> -nochargegp flag as per the tutorial, is this flag still valid while 
> generating toplogies.

CHARMM does not use charge groups.  Therefore, each atom should be its own 
"group" in the topology.  Using -nochargegrp overrides the default behavior of 
the .rtp files (which has multi-atom charge groups, although I think this was 
changed somewhere along the way, but I don't remember if it was before or after 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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