[gmx-users] Hi...

[Navratna Vajpai]

You are right .. I have used g_rama for the phi-psi values. I will  
try g_angle as well. With -ve i meant negative values for the phi angle.
As far as I understand negative phi values are sterically  not  
allowed. let me check with the g_angle as well.
Thanks for the answer as well the reference.
best regards
Nav


On Sep 14, 2006, at 4:22 PM, David van der Spoel wrote:

> 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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*******************************************
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
	       +41 78 744 0810(M)

navratna.vajpai at unibas.ch



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