[gmx-users] x2top problem

[Daan van Aalten]

Hi Eviatar

Why not try PRODRG?
see bottmo of e-mail for address.
There is now a version for > 100 atoms, will be on the server in a few
days after some more testing.

cheers

Daan

On Wed, 23 Jan 2002, Eviatar Tron wrote:

> hi,
> I am running x2top on a pdb file I created myself, which
> is composed of aromatic rings, so I tried using either CB or C
> atom types. I am tring to bypass the pdb2gmx which gives me
>  an error about the residue, which, as can be understood, 
> is unknown - not in the database. 
> so when I run x2top:
> 1. it is unhappy unless I specify both -o & -r options,
> if I only give it the -o,  it says I must specify at least one output file
> 2. if I choose the gromacs forcefield, it complains the following:
> > Fatal error: No forcefield type for atom C (1) with 0 bonds
> (I have CONECT entries which have been checked to
> produce the molecular structue on PDB viewers)
> 3. choosing a gromos force field results in the program
> running on 99% CPU time, for at least 15 minutes, without
> any sign of results - should it take so long?
> and if so, I suggest putting an indicator of some sort
> 	thanks (and many thanks to Eric ;) )
> 		Eviatar
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD 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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