AMBER Archive (2008)

Subject: AMBER: using amber ports in Gromacs

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Sun May 25 2008 - 13:28:26 CDT

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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