Dear Jason
thanks for the patch. It works well and solved the problem.
Jacopo
Inviato da iPad
> Il giorno 04/ott/2013, alle ore 13:07, Jason Swails <jason.swails.gmail.com> ha scritto:
>
>> On Fri, Oct 4, 2013 at 4:18 AM, Jacopo Sgrignani <sgrigna.gmail.com> wrote:
>>
>> Dear all
>> I'm trying to run MMPBSA Qm/MM calculations but I have some problems:
>>
>> 1) Even though I define ligand, receptor and complex qm-charge the
>> program ignores these numbers and the qm-charge unspecified in the
>> generated inputs file.
>>
>> 2) To overcome the first problem, I tried to use -make-mdins and then
>> -use-mdins putting the charge in the generated files.
>> However when I use the -use-mdins command the existing inputs are
>> automatically deleted.
>> I'm using my personal workstation so I can exclude automatic cleaning
>> procedure.
>>
>> Can you help me?
>
> I was able to reproduce your problem, and I have a solution that appears to
> work. Please apply the attached patch, rebuild MMPBSA.py, and try again.
> The following steps should do everything (assuming you put mmpbsa.patch in
> $AMBERHOME):
>
> cd $AMBERHOME
> ./update_amber --apply mmpbsa.patch
> make -C AmberTools/src/mmpbsa_py install
>
> That should reinstall MMPBSA.py without spending time rebuilding the rest
> of Amber (which this patch does not affect).
>
> If this patch works, I will roll it out as an update.
>
> Thanks for the report!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> <mmpbsa.patch>
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Received on Fri Oct 04 2013 - 05:30:05 PDT
