[gmx-users] mktop

[ram bio]

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.

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.

Thanks in advance,

Pramod


On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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