From: Srijita Paul (srijitap91_at_gmail.com)
Date: Sat Apr 16 2016 - 00:06:47 CDT
hi
i am trying to create a psf file for a system containing protein and urea
from psfgen.i am using the topology file top_all36_prot.rtf and the
topology file for urea is attached below.but i am getting the following
error
psfgen) building segment U
psfgen) reading residues from pdb file namd.pdb
psfgen) duplicate residue key 1
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 2
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 3
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 4
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 5
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 6
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 7
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 8
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 9
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 10
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 11
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 12
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 13
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 14
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) duplicate residue key 15
psfgen) ERROR: failed on residue UREA from pdb file
psfgen) extracted 2515 residues from pdb file
psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue SER:15
psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
in residue SER:15
psfgen) ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0)
CA(0) C(0) N(1)
in residue SER:15
psfgen) Warning: missing atoms for conformation SER CA-C-N-CA; skipping.
psfgen) Warning: missing atoms for conformation SER N-CA-C-O; skipping.
psfgen) Warning: missing atoms for conformation SER N-CA-C-N; skipping.
segment complete.
plz guide me if u can.i m a novish in namd.
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:01 CST