[gmx-users] Hi...

[David van der Spoel]

Navratna Vajpai wrote:
> Sorry for not so explicitly explaining the things.. Here it goes
> I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. 
> when I used the OPLS-AA the phi angles came out to be -ve for three of 
> the amino acids. which is stericaly not allowed. But when I ran it using 
> GROMOS I found all the phi-psi combinations with a negative phi value 
> distribution. But now I am lost as you have said it works only for 
> GROMOS like force field. Why?

problem in the anaysis program (assuming you used g_rama). please use 
g_angle.

> and if that so I have got -ve phi distribution for the other phi-psi plots. 
> My other question remained unanswered even now. Is there any way really 
> to judge which force field is to be chosen for particular type of analysis?
> Best regards 
> Thanks
>

what do you mean with -ve ?

force field can be evaluated in many ways.

Start by checking this paper and references in them:

Hydration thermodynamic properties of amino Acid analogues: a systematic 
comparison of biomolecular force fields and water models.

     * Hess B,
     * van der Vegt NF.

J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 
7;110(35):17616-26.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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