AMBER Archive (2006)

Subject: RE: AMBER: Radius of gyration

From: kepa koldo burusco (kepaquestions_at_yahoo.es)
Date: Fri Nov 24 2006 - 04:27:01 CST

[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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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

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

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