AMBER Archive (2006)

Subject: Re: RE: AMBER: Radius of gyration

From: Andy Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Fri Nov 24 2006 - 13:38:28 CST

Actually, (to answer your personal comment to Kepa, which has gone to
the whole list) I think that the question is of general interest to the
AMBER community.

And in that vein, do you not think it is polite to send a question in
english, as well as Spanish to an English mailing list!!

On Fri, 2006-11-24 at 19:25 +0100, Carles Jaime Cardiel wrote:
> kepa,
> Si respondes a alguien en concreto, no crees que no deberías enviarlo a la lista sino al interesado?????
> Un saludo,
> Carlos.
> ----------
> Carlos JAIME
> Catedràtic de Qca. Orgànica i Delegat del Rector per al Doctorat
> Dept. Química, Fac. Cièncias (Cn)
> Univ. Autònoma Barcelona
> 08193 Bellaterra (Barcelona)
> SPAIN
>
> ----- Missatge original -----
> De: kepa koldo burusco <kepaquestions_at_yahoo.es>
> Data: Divendres, Novembre 24, 2006 6:45 pm
> Assumpte: RE: AMBER: Radius of gyration
>
> > [24-XI-2006]
> >
> > Hi Andy,
> >
> > I've just checked the amber7, amber8, and amber9
> > versions of ptraj manuals. You were right when you
> > said that it calculates both the parameters but... I
> > still have doubts. I mean, amber9-ptraj really
> > calculates RMSD and Radius of Gyration. Nevertheless,
> > apparently, amber8-ptraj and amber7-ptraj are only
> > able to calculate RMSD.
> >
> > We usually work with amber7, and I was wondering... Is
> > it really true that amber7 and amber8 versions of
> > ptraj cannot calculate radius of gyration? Or maybe it
> > was ommited in the manual but still they were able to
> > do that?
> >
> > Any help??? I'm really interested, because we work
> > with amber7!!!
> >
> > Thank you very much in advance...
> >
> > Kepa K. Burusco
> >
> > PhD Student
> > Universidad Autónoma de Barcelona
> > BARCELONA (Spain)
> >
> > ###################################################
> >
> > --- Andy Purkiss-Trew
> > <a.purkiss_at_mail.cryst.bbk.ac.uk> escribió:
> >
> > > 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
> >
> >
> >
> >
> >
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-- 
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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