Dear Jason
I'm sorry to write another email but my colegues noted that, while in the MMPBSA.in file the qm charges are specified without decimal numbers (i.e. 1 2 3) the script produces input files with decimal numbers (1.0 2.0 etc..).
So we are able to run the calculations only manually editing the mdins files, because it seems that sander does not like decimal numbers in the input file.
Thanks again
Jacopo
> Il giorno 04/ott/2013, alle ore 14:34, Jason Swails <jason.swails.gmail.com> ha scritto:
>
>> On Fri, Oct 4, 2013 at 8:15 AM, Jacopo Sgrignani <sgrigna.gmail.com> wrote:
>>
>> Dear Jason
>> thanks for the patch. It works well and solved the problem.
>
> The patch should also fix -use-mdins with QM/MM input files.
>
> Thanks again for the report, I'll push this forward as an update.
>
> --Jason
>
>
>>
>> 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>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Oct 04 2013 - 07:00:04 PDT
