[gmx-users] modeling unnatural amino acids

Rich McClellan rich at chemistry.ucsc.edu
Mon Apr 22 23:17:40 CEST 2002


I have a peptide composed of unnatural amino acids that I'd like to
model with GROMACS.  GROMACS (pdb2gmx) is unable to calculate the
molecular topology of the system and gives an error message stating that
the residue is not found in the topology database.

Generating the topology file from hand looks daunting so I was wondering
if somebody has developed a topology database of "other" amino acids or
have suggestions on the best way to proceed.

		thanks in advance,

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