From: Santanu Chatterjee (santanu.chatter_at_gmail.com)
Date: Wed Sep 19 2007 - 18:24:38 CDT

Hi VMD users,
    I am trying to generate PSF file for decalanine molecule. I have
attached the PDB file with this email. I have the following psfgen input
file :
package require psfgen
topology top_all22_prot.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb alanine.pdb}
coordpdb alanine.pdb U
guesscoord
writepdb decala_wb.pdb
writepsf decala_wb.psf

When I try to generate the PSF file using VMD, I got the following screen
output :

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
 All comments to ADM jr. via the CHARMM web site: www.charmm.org
               parameter set discussion forum

Created by CHARMM version 22 1
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file alanine.pdb
unknown residue type CBX
extracted 12 residues from pdb file
Info: generating structure...
unknown residue type ACE
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

It seems to me that N terminus ACE is not recognized by Charmm 22 topology
file. I got the PDB file from NAMD examples. It had a PSF file based on
Charmm19 parameters.
I need to generate PSF file based on charmm22 parameters.
If anyone can tell me how to solve this problem, I will appreciate it.

Thanks,
Santanu