Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues

From: Giacomo Fiorin (
Date: Fri Dec 09 2016 - 12:34:43 CST

Hi Mark, I would definitely look first into the issue pointed out by the
error message:

On Fri, Dec 9, 2016 at 1:17 AM, Mark Hilge <> wrote:

> namd2 +p8 O3028-step1.namd > O3028-step1.log
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Problem reading grid force potential file
> Charm++ fatal error:
> FATAL ERROR: Problem reading grid force potential file
Take a look if your grid files (DX format) are present, and their contents
are not corrupted.

> Abort
> I do receive this error also when I am removing the symmetry restraints
> from the namd configuration file. Therefore, I am assuming that I am
> already doing something wrong when I create the psf or grid files
> from the pdb file with non-equal numbers of residues in the chains.
> Any help that resolves this problem is highly appreciated!
> Best wishes,
> Mark

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
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*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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