VMD-L Mailing List

From: jin (jin_at_mail.ku.edu)
Date: Tue Oct 26 2004 - 11:39:16 CDT

hello,
   I am trying to generate the pdb and psf file for protein 4HVP, but I am
getting errors using the psfgen command. I'll describe what I have done so
far.

1)I downloaded the pdb file for 4HVP and loaded in VMD, and generated hvpp.pdb
file for 4hvp without hydrogen bond.
2)I then try to create a psf file using a psfgen command on 'hvp.pgn' file I
generated from the NAMD tutorial file. I also downloaded the topology file
'top_all27_prot_lipid.inp'.

The script for hvp.pgn :
package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U {pdb hvpp.pdb}
coordpdb hvpp.pdb U
guesscoord
writepdb hvp.pdb
writepsf hvp.psf

3) when I type 'psfgen hvp.pgn', it gave me follow errors:

unknown residue type ABA
duplicate residue key PRO
duplicate residue key IGN

the list goes on with many duplicate residue keys and it ends saying the the
molecule was destroyed bay Fatal error. Is there something I'm doing wrong?
Please help, I appreciate it

                         thank you,jeremy