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
========================================
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