[gmx-users] Re: ligand force field parameters

m b mic0404 at yahoo.com
Fri Dec 12 12:54:00 CET 2003

> dear gmx-users,
> thanks
> 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
> studies.

dunno ... there should be plenty of papers out there ...

good luck!

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