Re: Question about AUTOGENERATE

From: Jim Phillips (
Date: Mon Nov 03 2003 - 21:43:56 CST


Psfgen is a black box implementation of a CHARMM topology file parser, and
it was based on the standard CHARMM 22/27 force field files. Therefore
it's not going to get some uncommon features or syntax right.

You can fix the autogenerate command by changing it to this:


The CHARMM 19 force field used explicit exclusions for some residues,
indicated by extra atom names on the ATOM line, such as (in TRP):

ATOM CG C -0.03 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2
ATOM CD2 C 0.10 NE1 CE2 CE3 CZ2 CZ3 CH2
ATOM CE2 C -0.04 CE3 CZ2 CZ3 CH2
ATOM CE3 CR1E -0.03 CZ2 CZ3 CH2

This is no longer the case with CHARMM 22/27, and therefore psfgen does
not implement explicit exclusions. It does (as of NAMD 2.5) notice that
these exclusions are present and ignores those atoms, which should
generate a fatal error if you try to use that residue.

If you need CHARMM 19 or some other topology with explicit exclusions, you
can still use CHARMM (the program) to build psf and pdb files, and NAMD
should handle the explicit exclusions correctly. If being able to do
explicit exclusions in psfgen is critical for your resesarch, let your
voices be heard and I'll look into it.


On Mon, 3 Nov 2003, Zhilei Chen wrote:

> Hi,
> I am a beginner of namd.
> I used the topology file from a previous paper as a exercise. It contains a
> command line
> I am not sure what it does, but when I use psfgen, it keeps popping up
> ERROR! Failed to parse autogenerate statement.
> ERROR! Explicit exclustions not supported, atom ignored.
> ERROR! Explicit exclustions not supported, atom ignored.
> ................
> Can anyone help me?
> I am stuck:(
> zhilei

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