[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 14 10:10:52 CET 2009

xiaowu759 at hotmail.com wrote:
> Dear,
>   As a small test, I want to simulate polystyene(PS) using GROMACS. 
> Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating 
> unit(320 atoms totally ) and add the STY residues to the .rtp files. 
> while running pdb2gmx, the procedure was finished "successfully". but I 
> find that only 16 atoms are in the generated .gro and .top files. Have 
> you met this strange thing? Or tell me what I should do with it?
The information you are sending here is not complete. How were termini
treated, hw was pdb2gmx invoked?
How do the building blocks in the rtp file and hdb file look like?

> Best regards,
> Chaofu Wu
> xiaowu759 at hotmail.com <mailto:xiaowu759 at hotmail.com>
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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