Re: FATAL ERROR Unknown parameter in charmm parameter file

From: Kenno Vanommeslaeghe (
Date: Mon Jul 01 2013 - 15:07:30 CDT

On 07/01/2013 02:19 PM, Cat Chenal wrote:
> /myfolder/toppar/v27/top_all27_prot_lipid.inp
> LINE=*27 1*

A topology file is not a parameter file. NAMD has no business with
topology files and doesn't know what to do with them. Topology files are
psfgen's business.

> If I remove this file (the other one I am using is a 'par' file), then I
> am missing a vdW parameter for some atoms, so I have to have it.

What you're saying is essentially that you "have to have" the above FATAL
ERROR in an early stage of your NAMD run because else you get a problem
with missing a vdW parameter in a later stage...

If you're missing a vdW parameter, then either you have to read a second
parameter file (probably the protein parameter file?) or something went
wrong during the psf generation.

By the way, it would be more optimal to use the CHARMM36 topology files
for psf generation and the CHARMM36 parameter files for NAMD simulation,
because there are important improvements in the force field, as mentioned
on this list a few days ago.

> Can someone give some light on how the version number/line is used?

Yes: it isn't.

> Also, are there specific guidelines for creating combined files?

Yes: don't. NAMD can read more than one parameter file. See my post of a
few days ago.



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