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

[N-J.M. Macaluso]

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