Hi,
I suspect that you are using an older version of cpptraj (check this
with 'cpptraj --version'). To use the 'radial' command in cpptraj you
should have version 12.0 or above (comes with AmberTools12, which is a
free download,
http://ambermd.org/AmberTools-get.html).
Note also that the 'radial' command in cpptraj is OpenMP parallelized;
if you have access to a multi-core machine you may want to take
advantage of that.
-Dan
On Tue, Sep 11, 2012 at 7:36 PM, Yanyan ZHU <zhuyanzily.gmail.com> wrote:
> Previously , you mentioned as the following : If you are using cpptraj you
> can add the'center1' keyword to calculate the RDF from the center of mass
> ofresidues 1 to 229 to all atoms in residues named WAT, e.g.
> radial 0.05 12 :1-229 :WAT center1
>
> According to this, my input file was rewritten as:
>
> trajin ***.mdcrd
>
> center origin :1-229
>
> image origin center
>
> radial 0.05 12 :1-229 :WAT center1
>
>
>
> the command during the calculation is：AMBERHOME/exe/cpptraj ***.prmtop
> rdf.in
>
>
>
> attention BEGIN TRAJECTORY PROCESSING:
>
> ----- [last20ns.mdcrd] (1-9901, 100) -----
>
> .... Setting up 2 actions for wat-wat.prmtop ....
>
> ...................................................
>
> [||||||||||||||||||||||||||||||||||||||||||||||||||] Complete.
>
>
>
> Read 100 frames and processed 100 frames.
>
>
>
> OUTPUT:
>
>
>
> DATASETS:
>
> There are no data sets.
>
> NO DATASETS WILL BE OUTPUT
>
>
>
> I would like to know whether my input file was wrong or the command was
> used in an unreasonable way. I haven’t found the tools which could
> calculate RDF in the test of cpptraj .I want to know whether cpptraj
> support RDF ? I am looking for your replay.
>
> Thank you for you help again .
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Sep 12 2012 - 08:30:03 PDT
