[gmx-users] pdb2gmx problem

David spoel at xray.bmc.uu.se
Wed Sep 4 18:48:07 CEST 2002

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
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> 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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