VMD-L Mailing List

From: Rima Chaudhuri (rima_chau_at_yahoo.com)
Date: Thu Jul 06 2006 - 11:05:50 CDT

Hi,
  I am still encountering the problem of generating a psf file from the attached pdb.
  It gives me the following errors Although the atoms do exist in the pdb. Secondly, it is trying to make a bond between the C(0) N(1) in residue ASN:299 when it should'nt!
   
  building segment U
reading residues from pdb file NL63.pdb
extracted 300 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.
ERROR: Missing atoms for bond C(0) N(1) in residue ASN:299
ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
 in residue ASN:299
Info: segment complete.
   
  If I use the autopsf functionality it does not give me any errors but later in the simulation the system gives me 'bad exclusion count error due to bad initial psf file.
  Please help!
   
  Thanks
  -Rima
  University of Illinois at Chicago
  Dept. of Bioengineering
  Bioinfomatics
  PhD candidate
  rchaud5_at_uic.edu
   
   

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