From: Peter Spijker (pspijker_at_wag.caltech.edu)
Date: Mon Mar 08 2004 - 12:23:12 CST
Hi Brian, and others,
This is the (reduced) error I encounter. Thanks for helping.
Greetz,
Peter
--- 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 <<<<<<<<<< from >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< and \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File /////// \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// Alexander D. MacKerell Jr. August 1999 All comments to ADM jr. email: alex,mmiris.ab.umd.edu 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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