[gmx-users] mktop

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 13 03:21:12 CEST 2011

ram bio wrote:
> Dear Justin,
> Thanks.
> The POPC bilayer i am using is with berger lipids, corrected for 
> dihedrals so as to be compatible with the OPLS FF for aminoacids.

I think significantly more parameters than just dihedrals need to be altered to 
make the Berger united-atom force field compatible with OPLS.

> While searching for the literature on compatibility of lipid FF and 
> protein FF, I found few references where similar modification was done 
> for DOPC lipid bilayer  and were suitable with various FF for proteins 
> and also with CHARMM FF:
> 1. Membrane protein simulations with a united-atom lipid and all-atom 
> protein model: lipid–protein interactions, side chain transfer free 
> energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234
> 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force 
> Fields.J Comput Chem 32: 1400–1410, 2011.
> I don't have the lipid bilayer with their  itp files with CHARMM FF 
> parameterization. Please could you inform me where to obtain them, so 
> that i can use the lipid bilayer structure for embedding the protein and 
> use the related CHARMM FF parameterised itp in the topology file in 
> gromacs for MD simulation.

The lipids are built into the CHARMM27 implementation in Gromacs.  You can 
generate their topology with pdb2gmx.  Run pdb2gmx on a single lipid, convert it 
to an .itp file, and #include it in the topology.  The CHARMM36 force field is 
also available in the User Contributions section of the Gromacs website.


> Thanks in advance,
> Pramod
> On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>     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
>     -- 
>     ==============================__==========
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>     ==============================__==========
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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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