[gmx-users] Re: ligand force field parameters
mic0404 at yahoo.com
Fri Dec 12 12:54:00 CET 2003
> dear gmx-users,
> 1. is there any resource(s) where i can find the force field parameters
> for different ligands
not really. To some limited extent the prodrg server does this job
(search google with keywords prodrg, gromacs) but these topologies
and the resulting force-fields are in mamy cases not really reliable,
in my humble opinion.
> 2. what are best ways to define such force field parameters that can be
> used along with receptors and membranes.
> 3.suppose if such parameters are not available to one such ligands of
> interest can some suggest me means of generating FF parameters.
The way I normally go is:
* use the OPLSAA force field
* calculate partial charges as ESPD charges with, e.g., ChelpG
in Gaussian (or anything compareable) for the ligand
(to be consistent this should also be done for the lipid/protein,
however, if these are too big then have to use the built-in OPLS charges)
* make a topology file for the ligand. Use for each residue/group in
your ligand intramolecular and LJ parameters you find for the same
or similar residues in amino-acids as given in the ffoplsaabon.itp
amd ffoplsaanb.itp files. This is the trickiest part requiring
some chemical intuition (and luck I'm afraid)
if you are unsure about how to make a topology file make one for a
simple peptide with pdb2gmx, than combine the relevant parts
in the ffoplsaa.rtp file and the topolgy files(s) created
by pdb2gmx and use that as a template.
... but only attempt doing this if you have loads of time
and a high "frustration tolerance level",
otherwise stick to prodrg and hope ...
> 4. re asking previous question best lipids can be used for GPCR simulation
dunno ... there should be plenty of papers out there ...
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