cyclic peptides

From: Austin B. Yongye (
Date: Mon Nov 03 2008 - 16:38:40 CST

Hi everyone,
I am trying to generate a cyclic peptide for NAMD simulations. I have the cyclic pdb structure with the N and C termini connected.
Here is my pgn file:

package require psf
topology top_all27_prot_lipid.rtf
segment U {pdb 5mer_noH.pdb}
coordpdb 5mer_noH.pdb U
writepdb 5mer_H.pdb
writepsf 5mer_H.psf

Every time I try to generate the psf file, the program disregards the connection between the 1st and 5th residues and addes 3H atoms to the N of residue 1 and carboxylic oxygen atoms to the C of the 5th residue.

I looked at the psf file and noticed this information in the header:

 REMARKS 2 patches were applied to the molecule.
 REMARKS topology top_all27_prot_lipid.rtf
 REMARKS segment U { first NTER; last CTER; auto angles dihedrals }
 REMARKS defaultpatch NTER U:1
 REMARKS defaultpatch CTER U:5

1). Is there a command I can use to tell the program not to treat the 1st and 5th residues as termini?
2). The topology file has patches for cyclic peptides, LIG1, etc but only for glycine residues. If someone other has done cyclic peptide simulations with NAMD I'll really appreciate any pointers.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:33 CST