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

From: Mark Hilge (markhilge_at_me.com)
Date: Mon Dec 12 2016 - 16:55:07 CST

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Dear Giacomo, dear Ryan,

Thanks a lot for your response! It’s running now. I think the problem was that I’ve used negative residue numbers
encoding a non-coding N-terminus. As consequence some files were created but empty.

Many thanks for your support!

Best wishes,

Mark

> On 09 Dec 2016, at 19:34, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> 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 <markhilge_at_me.com <mailto:markhilge_at_me.com>> 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
>
> Scholar: http://goo.gl/Q3TBQU <http://goo.gl/Q3TBQU>
> Personal: http://giacomofiorin.github.io/ <http://giacomofiorin.github.io/>
> Lab page: https://icms.cst.temple.edu/members.html <https://icms.cst.temple.edu/members.html>
>
> "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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