Re: query about the cross term in psf

From: Josh Vermaas (
Date: Sat Dec 06 2014 - 13:49:06 CST

Cross terms or dihedrals? The error is quite clear. You gave NAMD a psf
that had a dihedral (*not* a crossterm) term it did not recognize, and
to prevent you from doing something you didn't intend, it terminated for
you to avoid wasting computer time. Where did that term come from?
Grepping around in the charmm topology files, NR3 only shows up in
proteins, and HCL is an atomtype seen in lipids. Deleting terms
wholesale from a psf is a downright *dangerous* thing to do, as you will
no longer be simulating with a force field that has in any way been
validated. Is there something special about the system that needed a
linkage between proteins and lipids? If not, do you have any idea how
that dihedral term got into your psf?
-Josh Vermaas

On 12/06/2014 01:31 PM, Kshatresh Dutta Dubey wrote:
> Dear Users,
> I prepared the psf and corresponding pdb using vmd, but it gave error :
> 7427 7448)
> I googled the error and found somewhere that deleting the cross-terms
> in psf can make job to run. I did and job is running now. However, I
> am curious to know whether to delete cross-terms in psf is correct or
> not. Please suggest me.
> Thanks in advance.
> --
> With best regards
> ************************************************************************************************
> Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> Lise Meitner Center for Computational Quantum Chemistry
> Hebrew University of Jerusalem Israel
> Jerusalem, Israel

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