[gmx-users] Re: gmx-users digest, Vol 1 #804 - 10 msgs

[Daan van Aalten]

Hi Regina

I really don;t understand what the problem is. If you follow eactly the
PDF file on GROMACS-ligand simulations from the PRODRG FAQ these problems
don;t exist. be sure to take the PRODRG output PDB file **NOT** the
PDB file you put in, when you set up your system with pdb2gmx

No need whatsoever at any stage to do editing by hand

Daan

On Fri, 30 May 2003, Regina R. Monaco, Ph.D. wrote:

> 	You are correct - the problem lies with the "UNK" residues. I
> hand-edited the residue names and GROMACS atom types into the .pdb
> obtained from PRODRG2 and pdb2gmx ran ok.
>
> 	I am starting this calculation with a .mol file, which does not have
> any residue information - just coordinates. I am not really fond of the
> idea of hand-editing these peptide files as a working solution, so does
> anyone know of a way I can take a .mol file and have some GROMACS or
> some other software recognize, or allow me to graphically edit, the
> residues and atom types?
>
> Thanks,
> Regina
>
>
>     8. Re: Fwd: [gmx-users] D-form amino acids (Christoph Freudenberger)
>
> Message: 8
> Date: Fri, 30 May 2003 07:54:41 +0200
> From: Christoph Freudenberger
> <christoph.freudenberger at chemie.uni-ulm.de>
> Organization: University of Ulm
> To: gmx-users at gromacs.org
> Subject: Re: Fwd: [gmx-users] D-form amino acids
> Reply-To: gmx-users at gromacs.org
>
> Regina R. Monaco, Ph.D. wrote:
> > Hi Daan-
> >
> >     Well, **I** am not worried, but GROMACS won't accept the
> > calculation.  I am assuming the reason is that the program is not
> > certain what the  atom types are, what charges to use, and how to index
> > the molecule. At  least, thats what the error messages indicate  :>
> >
>
> Sound more like somethings wrong with the topology rather then
> the 'UNK' residues.
> Please post the error message and a few lines of the coordinate file.
>
> regards
> --
> Christoph Freudenberger
> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
>
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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

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