From: rasti (rasti_at_ut.ac.ir)
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
psfgen

psfcontext reset
topology top_all27_prot_lipid_modified.rtf

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

writepdb cyclic.pdb

any help is really appreciated,

Behnam