VMD-L Mailing List
From: rasti (rasti_at_ut.ac.ir)
Date: Sun Aug 25 2013 - 14:52:40 CDT
- Next message: Josh Vermaas: "Re: problem with building psf file"
- Previous message: Axel Kohlmeyer: "Re: VMD script"
- Next in thread: Josh Vermaas: "Re: problem with building psf file"
- Reply: Josh Vermaas: "Re: problem with building psf file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Josh Vermaas: "Re: problem with building psf file"
- Previous message: Axel Kohlmeyer: "Re: VMD script"
- Next in thread: Josh Vermaas: "Re: problem with building psf file"
- Reply: Josh Vermaas: "Re: problem with building psf file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]