'mass' is not a valid keyword for 'radial', so cpptraj assumes you
want to name your output data sets "mass" and complains when there are
two. The 'centerX' keywords for 'radial' are geometric center only.
See the manual for full details.
-Dan
On Sat, Sep 16, 2017 at 8:04 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> Thank you, Sir, for your kind response. For RDF calculation to calculate RDF
> plot between the center of mass of a residue I use this command :
> radial 0msr-deoxy-bb-rdf-test1.dat .1 35.0 :17-22
> :1-15.P,OP1,OP2,O5',C5',H5',C4',H4',C1',H1',C3',H3',C2',H2',H22'',03' volume
> center2 mass
> (source http://home.chpc.utah.edu/~cheatham/ptraj.html )
> There is an error :
> CPPTRAJ: Trajectory Analysis. V15.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 09/16/17 17:20:19
> | Available memory: 1547.42 MB
>
> Reading '1rde-0m.prmtop' as Amber Topology
> INPUT: Reading Input from file new-rdf.in
> [trajin qdna-1-130.mdcrd ]
> Reading 'qdna-1-130.mdcrd' as Amber Trajectory
> [radial 0msr-deoxy-bb-rdf-test1.dat .1 35.0 :17-22
> :1-15.P,OP1,OP2,O5',C5',H5',C4',H4',C1',H1',C3',H3',C2',H2',H22'',03' volume
> center2 mass ]
> RADIAL: Calculating RDF for atoms in mask [:17-22] to atoms in mask
> [:1-15.P,OP1,OP2,O5',C5',H5',C4',H4',C1',H1',C3',H3',C2',H2',H22'',03']
> Output to 0msr-deoxy-bb-rdf-test1.dat.
> Using center of atoms in mask2.
> Histogram max 35.000000, spacing 0.100000, bins 350.
> Normalizing based on cell volume.
> [radial 0msr-deoxy-bb-rdf-test.dat .1 35.0 :17-22
> :1-15.P,OP1,OP2,O5',C5',H5',C4',H4',C1',H1',C3',H3',C2',H2',H22'',03' volume
> center2 mass]
> Warning: DataSet 'mass' already present.
> Error: Could not allocate RDF data set.
> Error: Could not initialize action [radial]
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0809 seconds.
>
> Can u tell me what should I do ??
>
> Thanks
>
> Saikat
> On Saturday 16 September 2017, 5:16:35 PM IST, Daniel Roe
> <daniel.r.roe.gmail.com> wrote:
>
>
> Geometric center is the averaged position not taking into account mass,
> like center of mass when the mass of all elements is the same.
>
> -Dan
>
> On Sat, Sep 16, 2017 at 6:32 AM Saikat Pal <saikatpaliitg.yahoo.com> wrote:
>
>> Dear all,
>> In radial command (amber 2015 reference manual page no 586) there is
>> "center" word present. Calculate RDF from geometric center of atoms in
>> <solvent mask1> to all
>> atoms in <solute mask2>. Is geometric center of atoms same as center of
>> mass, if not then what is it ??
>> Thanks and regards,
>> Saikat
>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 18 2017 - 11:30:03 PDT
