generating psf & energy calculation for unusual amino acid - Aib

From: balaji nagarajan (balajisethu_at_gmail.com)
Date: Thu Nov 06 2008 - 21:57:17 CST

Dear users ,

i have a problem in namd to generate psf and energy
for an unusual aminoacid , Aib .
when i run
it gives a error
reading topology file top_all22_prot.inp

>>>>>>>>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
building segment U
reading residues from pdb file filen
unknown residue type AIB
unknown residue type AIB
extracted 10 residues from pdb file
Info: generating structure...
unknown residue type AIB
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.
1.2
ERROR) Could not read file file.psf
Unable to load file 'file.psf' using file type 'psf'.
There is no 'top' molecule in atomselect's 'molId'
There is no 'top' molecule in atomselect's 'molId'
can't read "sel1": no such variable
can't read "sel1": no such variable
Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
Info) Exiting normally.

HELP me out to fix the problem !

thank you

cris

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:04 CST