A question regarding generate pdb and psf file

From: Grace Shen (Lingling.Shen_at_bnpi.com)
Date: Tue Dec 06 2005 - 11:06:27 CST

Dear All:

I have a.pdb and a.psf files which works fine. In a.pdb file, it contains
two ligands and a receptor complex. Now I want to remove one ligand
information from a.pdb file. How can I generate corresponding psf file? What
I did is stated as followings:
1. Use VMD to modify the a.pdb file to remove the ligand and save as
btemp.pdb file.
2. Use btemp.pgn script to generate b.pdb and b.psf file.
package require psfgen
#topology lig12.rtf
topology lig2.rtf
topology /home1/lshen/Script/charmmInsightII/AMINOH.RTF
topology /home1/lshen/Script/charmmInsightII/CHARMM_support.rtf
segment U {pdb btemp.pdb}
coordpdb btemp.pdb U
writepdb b.pdb
writepsf b.psf
3. But I got the following error messages:
Created by CHARMM version 22 0
building segment U
reading residues from pdb file eg5cw.pdb
duplicate residue key 16
ERROR: failed on residue GLY from pdb file
duplicate residue key 19
ERROR: failed on residue ILE from pdb file
duplicate residue key 20
ERROR: failed on residue GLN from pdb file
duplicate residue key 25
ERROR: failed on residue CYS from pdb file
duplicate residue key 26
ERROR: failed on residue ARG from pdb file



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