From: surendra negi (negi009_at_yahoo.com)
Date: Mon Nov 01 2004 - 17:58:12 CST
Note: forwarded message attached.
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attached mail follows:
Hi,
I am getting following error when running psfgen
utility of NAMD. Though it is creating the pdb and psf
files, but I missing following atoms from original PDB
file. Any solution!
best, sn
----------
Here is an example:
PSFGEN from NAMD 2.5 for Linux-i686
reading topology file toppar/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
aliasing residue HIS to HSD
aliasing residue ILE atom CD1 to CD
aliasing residue GLY atom OXT to OT1
aliasing residue ARG atom OXT to OT1
building segment TBE
reading residues from pdb file x.pdb
extracted 341 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of
segment.
Info: skipping conformation C-N-CA-C at beginning of
segment.
Info: skipping conformation C-CA-N-HN at beginning of
segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of
segment.
Info: skipping conformation N-CA-C-O at end of
segment.
Info: skipping conformation N-CA-C-N at end of
segment.
Info: segment complete.
reading coordinates from pdb file x.pdb for segment
TBE
Warning: failed to set coordinate for atom HN2 MET:1
TBE
Warning: failed to set coordinate for atom HN3 MET:1
TBE
Warning: failed to set coordinate for atom HN1 MET:1
TBE
Warning: failed to set coordinate for atom HB3 MET:1
TBE
Warning: failed to set coordinate for atom HG3 MET:1
TBE
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