Thank you very much Dan for your kind support,
best regards
Alfredo
El 17/04/2012 11:35, Daniel Roe escribió:
> Hi,
>
> On Tue, Apr 17, 2012 at 10:22 AM, Alfredo Quevedo
> <alfredoq.fcq.unc.edu.ar> wrote:
>> Dan, as you state I assumed that "closeswaters" and "closest" are the
>> same. However I get different results with the same script:
>
> OK, I understand now - and yes you're right, the behavior is different
> - the ptraj version of the command strips only waters, while the
> cpptraj command strips everything not in the mask. This was an
> oversight on my part when I originally ported the command. A patch
> will be released soon for cpptraj that will make the behavior
> consistent with ptraj. Thanks again for the report.
>
> -Dan
>
>
>>
>> 1) ptraj input:
>>
>> ***********************************************************
>>
>> trajin complex.mdcrd 1 10
>> center :1-554
>> image center familiar
>> strip :Na+
>> closestwaters 10 :LIG
>> trajout complex_closestWAT.mdcrd trajectory
>>
>> ***********************************************************
>>
>> with this output I get the trajectory containing the whole complex with
>> 10 molecules sorrounding the ligand.
>>
>>
>> 2) cpptraj input
>>
>>
>> ******************************************************
>>
>> complex.mdcrd 1 10
>> center :1-554
>> image center familiar
>> strip :Na+
>> closest 10 :LIG first closestout fila.dat outprefix closest
>> trajout complex_closestWAT.mdcrd trajectory
>>
>> ******************************************************
>>
>> In this case I get a trajectory containing only the ligand sorrounded by
>> 10 water molecules.
>>
>>
>> best regards
>>
>> Alfredo
>>
>>
>>>
>>> Hi,
>>>
>>> On Tue, Apr 17, 2012 at 8:44 AM, Alfredo Quevedo
>>> <alfredoq.fcq.unc.edu.ar> wrote:
>>>> The point is that the calculation of distances is
>>>> rather slow, that is why I wanted to run it in parallel using cpptraj.
>>>> Unfortunately I find that the "closestwater" command is not included in
>>>> cpptraj.
>>>
>>> I'm confused by this. The 'closest' command is the same as the
>>> 'closestwater' command. In ptraj 'closestwater' was just the longer
>>> name for the shorter alias 'closest'. So in that sense 'closestwater'
>>> is in cpptraj, just now it is called 'closest'. In addition, this
>>> command is one of the actions in cpptraj that is OpenMP parallelized;
>>> let me know if you have problems compiling with OpenMP or getting the
>>> OpenMP version of cpptraj to work correctly.
>>>
>>> -Dan
>>>
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>>>
>>
>> --
>> ************************************************************************
>> Dr. Mario Alfredo Quevedo.-
>> Departamento de Farmacia.-
>> Facultad de Ciencias Químicas.-
>> Universidad Nacional Córdoba.-
>> 5000 Córdoba, Argentina
>> TE: 54351 4334163 Ext: 106
>>
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--
************************************************************************
Dr. Mario Alfredo Quevedo.-
Departamento de Farmacia.-
Facultad de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: 54351 4334163 Ext: 106
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Received on Tue Apr 17 2012 - 08:00:05 PDT
