[gmx-users] editing parameters

[David van der Spoel]

On Thu, 2003-05-08 at 10:11, Daan van Aalten wrote:
> 
> Hi Regina
> 
> Have you tried the PRODRG server for you rligand?
> 
> http://davapc1.bioch.dundee.ac.uk/prodrg
> 
> charge calculation with QM programmes is an excellent idea - as long as
> you stick to the charge group concept (David - could you comment on this
> please?)
> 
I agree...

If you use too large charge groups you will need a very large cut-off
too. For PME it doesn't matter.

> cheers
> 
> Daan
> 
> On Wed, 7 May 2003, Regina R. Monaco, Ph.D. wrote:
> 
> > I am setting up a run to do a MD calculation, which includes a ligand
> > (ethidium cation) that pdb2gmx doesn't recognize.  Ethidium doesn't
> > contain any oddly-parameterized atom types.  I have used gaussian to
> > calculate the ethidium charges, but am not sure how to import those
> > charges into the parameter files. Various error messages received while
> > trying to run pdb2gmx have been (depending on force field tried):
> >
> > Fatal error: Atom C1 in residue ETH not found in rtp database   **OR**
> > Fatal Error: Residue "ET" not found in residue topology database
> >
> > as examples.
> >
> > What is the procedure for editing the rtp ?
> >
> > Thanks,
> > Regina Monaco
> >
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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
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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