[gmx-users] non-standard residue format

[David van der Spoel]

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
> Elena
> 
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-- 
David.
________________________________________________________________________
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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