[gmx-users] amber ports in gromas - bond length warning

[David van der Spoel]

N-J.M. Macaluso wrote:
> Hello,
> 
> I am using the Amber ports for Gromacs provided by the following 
> website: http://chemistry.csulb.edu/ffamber/
> 
> I would like to use the Amber99sb force field for the simulation of a 
> cyclic peptide, joined by a disulfide bond between terminal cysteine 
> residues. I think I am using the appropriate Amber residue notation in 
> the pdb file for each cysteine. The N-terminal cysteine is called NCYX 
> and the C-terminal cysteine is CCYX.
> 
> However, when I used pdb2gmx -ff amber99sb to get a .gro file, I receive 
> several Long Bond warnings. I am working with a minimized structure, so 
> I'm a bit confused as to why this is happening. Has anyone come up 
> against this problem before?
Have you checked the structure in Pymol or something like that?

> 
> Many thanks,
> 
> Max
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-- 
David van der Spoel, Ph.D.
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