Re: About error during creation of psf file

From: flavio seixas (
Date: Thu Apr 19 2012 - 13:48:42 CDT

Its look like you are trying to simulate an heme protein.

I worked with hemoglobin, an heme protein too.

I used the following script to generate tetrameric protein bonded to O2.

First of all I separate protein, heme and O2 into separated files.

Other wrong thing I saw into your post is that you are naming heme residue as HEM. In topology file you will see that heme residue must be named as HEME

I hope it can help.


package require psfgen

pdbalias residue HIS HSD
pdbalias atom ILE CD1 CD

segment A {pdb chainA.pdb}
segment B {pdb hemeA.pdb}
segment C {pdb chainB.pdb}
segment D {pdb hemeB.pdb}
segment E {pdb chainC.pdb}
segment F {pdb hemeC.pdb}
segment G {pdb chainD.pdb}
segment H {pdb hemeD.pdb}
segment I {pdb oxyI.pdb}
segment J {pdb oxyJ.pdb}
segment K {pdb oxyK.pdb}
segment L {pdb oxyL.pdb}

patch PLO2 I:143 B:142 A:87
patch PLO2 J:148 D:147 C:92
patch PLO2 K:143 F:142 E:87
patch PLO2 L:148 H:147 G:92

coordpdb chainA.pdb A
coordpdb hemeA.pdb B
coordpdb oxyI.pdb I
coordpdb chainB.pdb C
coordpdb hemeB.pdb D
coordpdb oxyJ.pdb J
coordpdb chainC.pdb E
coordpdb hemeC.pdb F
coordpdb oxyK.pdb K
coordpdb chainD.pdb G
coordpdb hemeD.pdb H
coordpdb oxyL.pdb L


writepdb R-Human.pdb
writepsf R-Human.psf

--- On Sat, 4/14/12, Vidhya Sankar <> wrote:

From: Vidhya Sankar <>
Subject: namd-l: About error during creation of psf file
To: "" <>
Date: Saturday, April 14, 2012, 7:28 AM

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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