RE: HEM residue in NAMD

From: Blake Charlebois (
Date: Tue Nov 02 2004 - 04:03:00 CST


Have you aliased HEM to HEME (similar to aliasing HIS to HSD or HSE, which
is described in one of the tutorials)? I expect the command would be this:
alias residue HEM HEME

If you do a search on HEME in the CHARMM topology file (assuming you are
using the CHARMM force field) you will find the residue and atom naming
conventions for HEME. In UNIX you would do this:
type (at the command prompt) less top_all22_prot.inp
press the / key
type HEME
hit enter

Somewhere out there you may find a document similar to with useful information about

Good luck,

-----Original Message-----
From: [] On Behalf
Of Peter Bazeley
Sent: November 2, 2004 3:24 AM
Subject: namd-l: HEM residue in NAMD


I need a little help here. I have a PDB file of HETATM
atoms for a heme group. Each atom has "HEM" in the PDB
residue column (I've attached the PDB file). I am
trying to generate a psf file, but get the following:

building segment HEME
reading residues from pdb file
unknown residue type HEM
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type HEM


ERROR: failed on end of segment
start over.
ERROR: failed on guessing coordinates
ERROR: failed on writing structure to psf file
ERROR: failed on writing coordinates to pdb file

There were quite a few coordinates that couldn't be
guessed, but I've had that problem before and was
still able to generate a psf file. Has anyone else
used a Heme group in a NAMD simulation, or know what I
am doing wrong?

Peter Bazeley

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