VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun Aug 25 2013 - 16:34:44 CDT

Hi Behnam,
The usual peptide-building tools assume a linear peptide, and so you'll
need to manually add the linkage between the first and last residue. The
important differences are around your segment definition:

segment U {
pdb peptide.pdb
auto none #You don't want the default protein behavior of adding a
N-terminal and C-terminal patch to the first and last residues
}
patch LINK U:lastresidueid U:1 #This does the patching.
coordpdb peptide.pdb U
regenerate angles dihedrals #Angles and dihedral terms across the patch
aren't specified in the topology file, so have psfgen regenerate them
automatically

Consult the psfgen userguide for the exact syntax (I'm operating off
memory, and probably got a detail wrong here or there), and replace the
lastresidueid with the actual id. :)

Good luck!
-Josh

On 08/25/2013 02:52 PM, rasti wrote:
>
> 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
>