Hello,
I have downloaded the Amber 99sb force field ports for implementation
in the gromacs program. I am trying to perform simulated annealing on
a cyclic peptide which is cyclized by a disulfide bond between two
terminal cysteine residues. I have named these two cysteine residues
NCYX and CCYX, respectively, in the .pdb file to specify them both as
terminal residues and as disulfide bonded residues. However, when I
use the pdb2gmx program using the amber force field files this results
in a system with nonphysical bonds (i.e. bonds are too long and the
system looks like it has exploded).
Any advice on implementing this amber force field in Gromacs is
appreciated!
Cristina
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Received on Wed May 28 2008 - 06:07:16 PDT
