[gmx-users] Re: ligand force field parameters

[Daan van Aalten]

Dear Michael

I would be very grateful if you could send me the ligands that did not
work for you in the PRODRG server - it will help us improve the program
(or, not uncommon, find the errors in your starting coordinates)

cheers

Daan


On Fri, 12 Dec 2003, m b wrote:

>
> > 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!
> Michael
>
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O