Hello David,
Thanks a lot for your reply.
As you've suggested, I've used the process_mdout.perl to retrieve
information from the mdout.ubiquitin.save file. For this one, the
summary.VOLUME file contains both the elapsed time and the volume, but
the summary.DENSITY file contains only the elapsed time..
I’ve double checked mi mdout file and it contains both volume
and density but neither are retrieved.. While doing so, I’ve
realised that these two weren’t in the same “place”
as in the mdout.ubiquitin.save file. May this be the issue?
Thanks for any further suggestion,
Ruth
> On 21 Jun 2016, at 19:25, David A Case <david.case.rutgers.edu> wrote:
>
> On Tue, Jun 21, 2016, Ruth Helena Tichauer wrote:
>>
>> When analysing my output files with the script “process_mdout.perl”, I
>> find that it is not retrieving the density, nor the volume, of my system
>> as both summary.DENSITY and summary.VOLUME files only contain the time
>> elapsed. Am I using an “old” version? You can find it in attachements.
>
> First, try process_mdout.perl on a sample mdout file like this one:
> $AMBERHOME/test/ubiquitin/mdout.ubiquitin.save.
>
> Second, as a sanity check, make sure you actually have Density and VOLUME
> lines in your mdout file.
>
> ...good luck...dac
>
>
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Received on Wed Jun 22 2016 - 06:30:03 PDT
