From: Pijush Ghosh (
Date: Fri May 27 2005 - 17:10:47 CDT

Could you please elaborate your problem little bit more, it sounds not that
serious a problem though, you can get rid of that by slightly adjusting the
residue names in your topology or pdb file, but I am not quite sure about
your problem.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA
-----Original Message-----
From: [] On Behalf
Of Wei Chen
Sent: Friday, May 27, 2005 3:11 PM
Subject: namd-l: PSFGEN

Hi, all,

I try to generate psf file from 1IGT.pdb. But there are duplicate
resid in the pdb file, like:

ATOM 3039 N TYR B 100I
ATOM 3040 CA TYR B 100I
ATOM 3041 C TYR B 100I
ATOM 3042 O TYR B 100I
ATOM 3043 CB TYR B 100I
ATOM 3044 CG TYR B 100I
ATOM 3045 CD1 TYR B 100I
ATOM 3046 CD2 TYR B 100I
ATOM 3047 CE1 TYR B 100I
ATOM 3048 CE2 TYR B 100I
ATOM 3049 CZ TYR B 100I
ATOM 3050 OH TYR B 100I
ATOM 3051 H TYR B 100I
ATOM 3052 HH TYR B 100I
ATOM 3053 N ALA B 100J
ATOM 3054 CA ALA B 100J
ATOM 3055 C ALA B 100J
ATOM 3056 O ALA B 100J
ATOM 3057 CB ALA B 100J
ATOM 3058 H ALA B 100J
ATOM 3059 N MET B 100K
ATOM 3060 CA MET B 100K
ATOM 3061 C MET B 100K
ATOM 3062 O MET B 100K
ATOM 3063 CB MET B 100K
ATOM 3064 CG MET B 100K
ATOM 3065 SD MET B 100K
ATOM 3066 CE MET B 100K
ATOM 3067 H MET B 100K

When I used psfgen to generate psf file, only first residue could be kept.
So what can I do to generate all residues?


Wei Chen


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