From: David Rogers (wantye_at_gmail.com)
Date: Wed Apr 18 2012 - 23:21:43 CDT
This error message means that there is a duplicate residue in the
pdb file you sent it. It can happen that two positions (say A and B
forms) are both in the pdb because they were identified as alternate
conformations present in the crystal. Look at your pdb file around
residue 142 for a residue with a number followed by A or B. Remove
one, get rid of A/B, and re-run. Always check that there all the
residues are contiguous when psfgen finishes (or a bond will stretch
and the simulation will crash at best). If you're new at this, read
through the namd psfgen tutorial and reference the user guide.
Your HEM residue is more of an issue, since you need special
forcefield parameters for anything other than the 20 common amino
acids and water (but people still debate about the water, and don't
get me started on ions). Either
1) get rid of it by deleting HEM from the pdb
or
2) check the PDB header for a description of what HEM is (maybe a
heme?) and then check the literature for what others have done to do
simulations with it.
~ David M. Rogers
Postdoc, Nanobiology
Sandia National Labs
On Sat, Apr 14, 2012 at 2:26 AM, Vidhya Sankar
<vidhyasankar7928_at_yahoo.com> wrote:
> Dear Namd user ,
> I am beginner of Namd when i run .pgn file in
> VMD terminal i got the following error could any one help me to solve the
> errror or at least pontout previous discussion of same error in the namd
> mailing list
>
> duplicate residue key 142
> ERROR: failed on residue ALA from pdb file
> duplicate residue key 143
> ERROR: failed on residue HIS from pdb file
> duplicate residue key 144
> ERROR: failed on residue LYS from pdb file
> duplicate residue key 145
> ERROR: failed on residue TYR from pdb file
> duplicate residue key 146
> ERROR: failed on residue HIS from pdb file
> unknown residue type HEM
> extracted 1149 residues from pdb file
> Info: generating structure...
> unknown residue type HEM
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> Thanks in advance
>
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