[gmx-users] pdb2gmx problem

[Daan Virtual]

Hi Alexander

Have you tried dropping your non-protein coordinates into the PRODRG
server and using the resulting GROMACS topologies?

See http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html

Daan

On 4 Sep 2002, David wrote:

> On Wed, 2002-09-04 at 16:20, alexander yakovenko wrote:
> > Hi All,
> > I have the next problem. I try to make the topology of the nonprotein molecule with 143 atoms. I found that pdb2gmx add some bonds which were not stored in rtp file, and some atoms leave separate. I check the topology manually (rtp file) and haven t fount any separated atoms in rtp.
> > Why pdb2gmx add and remove some bonds automatically?
> > Is my molecule too large?
> No, but you have to be more specific. Did you make an rtp entry for your
> molecule? If not then there is little hope that pdb2gmx will work.
>
> If you did and it doesn't work, please send the rtp entry (and hdb
> entry) + pdb file to the list..
> > Thank you,
> >
> > Alexander Yakovenko
> > Institute of Molecular Biology & Genetic of NAS of Ukraine
> > 03143
> > acad.Zabolotnogo str. 150
> > Kiev
> > Ukraine
> > ______________________________________________
> > E-mail: yakovenko_a at ukr.net
> >
> >
> >
> > _______________________________________________
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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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