RE: [gmx-users] Hi...

[Mu Yuguang (Dr)]

OPLS-aa force field is good for beta structure, it is not so good for alpha helix study. Amber99f force field is good for alpha helix , but not good for beta structure   Best regards Yuguang   Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php   From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Navratna Vajpai Sent: Thursday, September 14, 2006 9:50 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Hi...   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? 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   On Sep 14, 2006, at 3:36 PM, David van der Spoel wrote: Navratna Vajpai wrote: Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regards Nav Begin forwarded message: *From: *Navratna Vajpai <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 *To: *Discussion list for GROMACS users <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> *Subject: **[gmx-users] Hi...* *Reply-To: *Discussion list for GROMACS users <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>   Dear All Hi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field. As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't found that. I tried using the GROMOS96 and opls-aa force field on my small peptides for a period of 20ns and found that with opls-aa even the phi-psi combination of the individual amino acids were incorrect. Actually this always puzzled me to make a choice for the Force field.  The rest of the script was unchanged for the two runs. Could you please comment on the above results? Is there any way really to judge which force field is to be chosen for particular type of analysis? Best regards Nav       what do you mean with incorrect? your question is quite vague.   the g_rama program works only for GROMOS like force fields unfortunately but that doesn't mean the phi/psi are wrong. What would be the "correct" result anyway? Maybe your peptide unfolds.   --  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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