Re: Generate PSF structure

From: Peter Spijker (
Date: Mon Mar 08 2004 - 12:23:12 CST

Hi Brian, and others,

This is the (reduced) error I encounter. Thanks for helping.



PSFGEN from NAMD 2.5 for Linux-i686
reading topology file top_all27_prot_lipid.inp
>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,  <<<<<<<<<
  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
              Alexander D. MacKerell Jr.
                     August 1999
 All comments to ADM jr.  email: alex,
              telephone: 410-706-7442
Created by CHARMM version 27 1
building segment B2
reading residues from pdb file prot.pdb
unknown residue type HIS
unknown residue type HIS
unknown residue type HIS
unknown residue type HIS
unknown residue type HIS
extracted 271 residues from pdb file
Info: generating structure...
unknown residue type HIS
aliasing residue ILE atom CD1 to CD
reading coordinates from pdb file prot.pdb for segment B2
Warning: failed to set coordinate for atom N   GLY:1      B2
[... these warnings go on for a while ...]
Info: writing psf file nice.psf
Info: writing pdb file nice.pdb
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
ERROR: failed on guessing coordinates
ERROR: failed on writing structure to psf file
ERROR: failed on writing coordinates to pdb file

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