Hi Jason,
Sorry for not mentioning .. My topology is a regular AMBER topology
created a while ago with AMBER 9 (or 10 but I believe it was 9).
pamred.py works but I wanted to do everything in a cpptraj script ...
Just as a side notice, in parmed the mask "Cl=" does not work (actually
quotes are not allowed. "Cl-" works however fine. I am not sure this is
documented anywhere.
Best,
Vlad
On 11/13/2012 02:34 PM, Jason Swails wrote:
> On Tue, Nov 13, 2012 at 7:13 AM, Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
>> Dear Amber users,
>>
>> I noticed that the "parmstrip :WAT" command in cpptraj leads to a
>> segmentation fault at runtime (AMBER 12, AmberTools 12).
>> I run different tests and this behavior is specific to "parmstrip".
>> "strip :WAT" runs absolutely fine.
>>
> You can try parmed.py or xparmed.py to strip water from the topology file.
>
> Apart from this, I think we'll need to know more about your prmtop. Is it
> a chamber topology? In this case, I don't think either cpptraj or parmed
> will work.
>
> Good luck,
> Jason
>
>
>> Did any of you notice this ?
>>
>> Best wishes
>> Vlad
>>
>> --
>> Dr. Vlad Cojocaru
>> Max Planck Institute for Molecular Biomedicine
>> Department of Cell and Developmental Biology
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Tue Nov 13 2012 - 06:00:04 PST
