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

[David]

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.

> 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
-- 
Groeten, David.
________________________________________________________________________
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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