From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Apr 16 2016 - 20:14:41 CDT
We would need to see your pdb file and psfgen script to give good advice, but I’m guessing that the problem is that you have multiple residues with the same number in the same chain.
> On Apr 16, 2016, at 1:06 AM, Srijita Paul <srijitap91_at_gmail.com> wrote:
>
> 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.
> <top_urea.rtf>
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