Dan, as you state I assumed that "closeswaters" and "closest" are the
same. However I get different results with the same script:
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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Received on Tue Apr 17 2012 - 07:30:05 PDT
