[gmx-users] amber ports in gromas - bond length warning
N-J.M. Macaluso
njmm2 at cam.ac.uk
Sun May 25 22:53:04 CEST 2008
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?
Many thanks,
Max
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