From: rasti (
Date: Sun Aug 25 2013 - 14:52:40 CDT


Dear VMD/NAMD users,

iam trying to build psf file for a cyclic
peptide and i keep facing following problem:

1) when i use the pdb
relates to the cyclic form peptide (generated by hyperchem), VMD ignores
the cyclic structure and remove the peptide bond bond between the first
and the last residues adding extra O and N instead.

package require

psfcontext reset
topology top_all27_prot_lipid_modified.rtf

pdbalias atom ILE CD1CD
pdbalias residue HIS HSE
segment U {pdb
coordpdb peptide.pdb U
writepsf cyclic.psf

writepdb cyclic.pdb

any help is really appreciated,