Re: [AMBER] :Re: "closest" command in cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 17 Apr 2012 11:05:00 -0400

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


Received on Tue Apr 17 2012 - 08:30:02 PDT
Custom Search