<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">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. <DIV>[ Phi=180.0_2_33.5 ] or [ Phi=0.0_3_3.77 ] </DIV><DIV>Please suggest.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>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?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Best regards </DIV><DIV>Nav</DIV><DIV><BR><DIV><DIV>On Sep 14, 2006, at 4:22 PM, David van der Spoel wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Navratna Vajpai wrote:</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sorry for not so explicitly explaining the things.. Here it goes</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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?</DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">problem in the anaysis program (assuming you used g_rama). please use g_angle.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Best regards Thanks</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">what do you mean with -ve ?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">force field can be evaluated in many ways.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Start by checking this paper and references in them:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hydration thermodynamic properties of amino Acid analogues: a systematic comparison of biomolecular force fields and water models.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>* Hess B,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>* van der Vegt NF.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep 7;110(35):17616-26.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">David.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">________________________________________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Husargatan 3, Box 596,<SPAN class="Apple-converted-space"> <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phone:<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>46 18 471 4205<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>fax: 46 18 511 755</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>spoel@gromacs.org <SPAN class="Apple-converted-space"> </SPAN>http://folding.bmc.uu.se</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. 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D student in Prof. Grzesiek's laboratory</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Department of Structural Biology</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Biozentrum, University of Basel</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Klingelbergstrasse 70,</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">CH-4056</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Basel, Switzerland.</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Phone- +41 61 267 2080(O)</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-tab-span" style="white-space:pre; font-family: Helvetica; "><SPAN class="Apple-style-span" style="white-space: pre; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="white-space: pre; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; white-space: pre; "><SPAN class="Apple-style-span" style="font-family: Helvetica; white-space: pre; "> </SPAN></SPAN></SPAN></SPAN></SPAN><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "> +41 78 744 0810(M)</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><A href="mailto:navratna.vajpai@unibas.ch">navratna.vajpai@unibas.ch</A></SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></DIV></DIV></BODY></HTML>