Re: [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 [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* 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) [EMAIL PROTECTED]

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