Dan, I applied the patch and now I obtain the same trajectory as in
ptraj with 'closestwaters'.
Thank you very much for the help,
regards
Alfredo
El 17/04/2012 12:05, Daniel Roe escribió:
> Hi,
>
> If you would like to test this, I have prepared a patch (attached)
> which should make the behavior of cpptraj 'closest' match ptraj. If
> you do try it, please let me know if it works and/or if you have any
> questions.
>
> Apply it from AMBERHOME:
>
> cd $AMBERHOME
> patch -p0 -N< Action_Closest.patch
>
> You should see these messages if the patch installs correctly:
>
> patching file AmberTools/src/cpptraj/src/Action_Closest.cpp
> patching file AmberTools/src/cpptraj/src/Action_Closest.h
>
> Let me know if there is any other way I can help.
>
> -Dan
>
> On Tue, Apr 17, 2012 at 10:37 AM, Alfredo Quevedo
> <alfredoq.fcq.unc.edu.ar> wrote:
>> 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
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>> ----- Terminar mensaje reenviado -----
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------
>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> ************************************************************************
>>>> Dr. Mario Alfredo Quevedo.-
>>>> Departamento de Farmacia.-
>>>> Facultad de Ciencias Químicas.-
>>>> Universidad Nacional Córdoba.-
>>>> 5000 Córdoba, Argentina
>>>> TE: 54351 4334163 Ext: 106
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>> --
>> ************************************************************************
>> Dr. Mario Alfredo Quevedo.-
>> Departamento de Farmacia.-
>> Facultad de Ciencias Químicas.-
>> Universidad Nacional Córdoba.-
>> 5000 Córdoba, Argentina
>> TE: 54351 4334163 Ext: 106
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
--
************************************************************************
Dr. Mario Alfredo Quevedo.-
Departamento de Farmacia.-
Facultad de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: 54351 4334163 Ext: 106
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 17 2012 - 08:30:03 PDT
