What are the atoms involved in the Long Bond waring?
For cyclic peptide, you also need to hand edit the topology file after
pdb2gmx to connect the last residue to the first residue.
Regards,
Yang Ye
David van der Spoel wrote:
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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