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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