From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 09 2014 - 21:50:21 CST

On Jan 9, 2014 9:52 PM, "Tristan Croll" <tristan.croll_at_qut.edu.au> wrote:
>
> Hi,
>
>
>
> Iíve added the option to include secondary structure restraints to my
gradually developing interactive MDFF extension (built from AutoIMD), and
have run into a rather odd (and intermittent) problem.
>
>
>
> The call to ssrestraints in the code is fairly straightforward:
>
>
>
> # If secondary structure restraints are chosen, create restraints file
>
> if $settings::usessrestraints {
>
> package require ssrestraints
>
> ssrestraints -psf [file join "$settings::scratchdir" automdff.psf]
-pdb [file join "$settings::scratchdir" automdff.pdb] -sel
"$settings::ssrestraintsseltext" $settings::restrainhbonds -o [file join
"$settings::scratchdir" automdff-ssrestraints.txt]
>
> mol delete top
>
> }
>
>
>
> ... as is the addition to the namd template file:
>
>
>
> # use secondary structure restraints if required
>
> if $usessrestraints {
>
> extraBonds yes
>
> extraBondsFile automdff-ssrestraints.txt
>
> }
>
>
>
> Iíve checked, and it creates a perfectly normal looking extrabonds file.
However, when I run it, roughly 3 times out of 4 I get an ďabnormal EOFĒ
error with the diagnostic giving a line partway through
automdff-ssrestraints.txt. The interesting thing is that itís always
truncating some power of two (2048, 4096 or 8192) characters into the file
Ė which would suggest that a too-small chunk of memory is being
pre-assigned for the file. But in that case, why does it vary from run to
run (with identical conditions)?
>

This sounds more like a file not being properly closed to me.

Axel.

>
>
> Iím happy to send anyone a copy of the code to see if you can replicate
the bug.
>
>
>
> Tristan Croll
>
> Lecturer
>
> Faculty of Health
>
> Institute of Health and Biomedical Engineering
>
> Queensland University of Technology
>
> 60 Musk Ave
>
> Kelvin Grove QLD 4059 Australia
>
> +61 7 3138 6443
>
>
>
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