[gmx-users] Re: gmx-users digest, Vol 1 #804 - 10 msgs
spoel at xray.bmc.uu.se
Fri May 30 18:11:01 CEST 2003
On Fri, 2003-05-30 at 16:43, 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?
you could try molden, but otherwise I wouldn't know.
> 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.
Dr. David van der Spoel, Dept. of Cell and Molecular 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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