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.

-Justin

Thanks in advance,

Pramod


On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@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
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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