navratna.vajpai at unibas.ch
Thu Sep 14 18:08:09 CEST 2006
As suggested by you I tried using the g_angle. But got tucked. It
asks for a .ndx file. I tried making it using mk_angndx but gave me
an error when i used the option -type phi-psi. Although it worked
well when I used the option dihedral instead of phi-psi. The .ndx
file has strange nomenclature which i didn't followed.
[ Phi=180.0_2_33.5 ] or [ Phi=0.0_3_3.77 ]
As you said problem with the analysis program g_rama. I looked for
g_rama as well as g_chi .. its mentioned in the g_chi option that the
phi psi calculation are different from the conventional calculations.
Instead of C'(i-1)-Ni-CAi-C'i , H-N-CA-C' is used and similarly its
different for the psi as well. But it also states that it is
different from the g_rama. I was wondering what other atoms are taken
for the phi-psi calculations?
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 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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Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Phone- +41 61 267 2080(O)
+41 78 744 0810(M)
navratna.vajpai at unibas.ch
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