[gmx-users] mktop

[Justin A. Lemkul]

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 
4.5.4).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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