[gmx-users] non-standard residue format
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 24 17:41:58 CEST 2004
On Thu, 2004-06-24 at 17:37, Elena Molteni wrote:
> Dear gmx users,
> I have to simulate a peptide containing non-standard aminoacids, some of
> which have names consisting of 5 characters in the gromacs "rtp" file
> (library). When I use pdb2gmx in order to build the topology from the pdb
> file, the program considers the last character of the residue name as a
> chain identifier. If I shift the residue name one space back in the pdb
> file, the program reads this name starting from its second character (and
> gives an error).
> How can I put these 5-character-residue names in my pdb file, in order to
> run pdb2gmx on it?
you can not use more than 4 characters. you'll have to abbreviate.
> thanks in advance
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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