AMBER Archive (2006)

Subject: RE: AMBER: Radius of gyration

From: Andy Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Fri Nov 24 2006 - 06:58:53 CST

Hi Rosajann and Kepa,

ptraj is able to calculate radius of gyration, as well as rmsd. See the
keyword radgyr in the manual. It can also calculate the radius of
gyration for part of the molecule, using masks.

The atomicfluct option may also be of interest when looking at per
residue fluctuations of the protein.

Hope this is of help

Andy

On Fri, 2006-11-24 at 11:27 +0100, kepa koldo burusco wrote:
> [24-XI-2006]
>
> Hi rosajaan,
>
> I had the same problem last week (at least so I
> think). I needed to calculate the radius of giration
> and the RMSD for some molecules. I intended to do it
> with ptraj but the option was not available. I was
> told to use CARNAL, and after fighting hard with it, I
> managed to run the calculation.
>
> Try to customize the files attached to this e-mail to
> your needs. You will probably need to adjust some
> lines to define your atoms/residues/ etc: Try to check
> AMBER 7 manual, page 219, to the bottom (DECLARE
> paragraf).
>
> If you need to previously remove water solvent from
> the box, its better you to use ptraj (I find it really
> easier than CARNAL).
>
> I know, handling CARNAL is a big nightmare, but I
> don't know wether exists another possibility. We will
> have to wait until some brave programmer decides to
> include these useful options into ptraj.
>
> Good Luck!!!
>
>
> Kepa K. Burusco
>
> PhD Student
> Department of Chemistry.
> Universidad Autónoma de Barcelona
> BARCELONA (Spain)
>
> *************************************************
>
> --- "r. a." <rosajaan_at_yahoo.com> escribió:
>
> > Dear All
> >
> > Hi...
> > Could anybody introduce me any alternative for
> > calculating radius of gyration and RMSD plot vs.
> > residue number except than carnal...
> >
> > Regards
>
>
>
> ______________________________________________
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> plain text document attachment (carnal_RMSD.in.txt),
> "567906580-carnal_RMSD.in.txt"
> FILES_IN PARM p1 /disk9/kepa/myMoleculeName.top; STREAM s1 /disk9/kepa/myMoleculeName.trj; STATIC refConf /disk9/kepa/myMoleculeName.rst; FILES_OUT TABLE tab1 myMoleculeName_RMSD.txt; DECLARE GROUP grp1 ( RES NAME residueName01 residueName02 residueName03 ); RMS fit1 FIT grp1 s1 refConf; OUTPUT TABLE tab1 fit1; END
> plain text document attachment (carnal_RadiusOfGyration.in.txt),
> "823525471-carnal_RadiusOfGyration.in.txt"
> FILES_IN PARM p1 /disk9/kepa/myMoleculeName.top; STREAM s1 /disk9/kepa/myMoleculeName.trj; FILES_OUT TABLE tab1 myMoleculeName_radGyr.txt; DECLARE GROUP grp1 ( RES NAME residueName01 residueName02 residueName03 ); OUTPUT TABLE tab1 grp1%radgyr; END 

-- 
Cat, n.: Lapwarmer with built-in buzzer.
+----------------------------------------------------------------------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                    |
|      Phone 020 7631 6869 (Work) or 07763 490 360 (Mobile)            |
+----------------------------------------------------------------------+

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