<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Many thanks Eric, it worked. I didn't really had look into this.<DIV>Best regards</DIV><DIV>Nav</DIV><DIV><BR><DIV><DIV>On Aug 16, 2006, at 11:34 AM, Erik Marklund wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote:</DIV> <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; ">Hey Mark..</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I had attached the file along with the mail. I think you could<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">not receive it. let me paste the contents and explain it little more.<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am trying to run the simulation in vacuum of a nona peptide. I managed<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to get pdb2gmx working and even further the EM working. But when I tried<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to do the MD run after a small minimization of protein, I got an error<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">message after the execution of grompp. The execution asked for the -n<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">option which indicates for the index file. 1) I don't know why it asked for?</DIV> </BLOCKQUOTE></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; ">My guess it's because of this line in the mdp file:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">tc-grps <SPAN class="Apple-converted-space"> </SPAN>=<SPAN class="Apple-converted-space"> </SPAN>protein<SPAN class="Apple-converted-space"> </SPAN>sol</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; ">Apparently you have temperature-coupled the solvent, even though you</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">have no solvent. Vacuum, right? Note that grompp is looking for 'sol'</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and, when it can't find it among the default groups (see manual), it</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">looks for an index file:</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; ">Fatal error:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Group sol not found in indexfile.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Maybe you have non-default goups in your mdp file, while not using the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'-n' option of grompp.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">In that case use the '-n' option.</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; ">Try removing 'sol' from the mdp file. If you are simulating in vacuum,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">you (probably) have no solvent.</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; ">/Erik</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BLOCKQUOTE type="cite"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2) If it ask for is there any way to solv this problem. Actually i tried<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">using that also. But the error stayed back.<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am also pasting the error after the grompp. Somehow this could not<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">prepare the input file for the MD run.<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">3) third question is: I am wondering whether i can start my run just<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">after the execution of pdb2gmx. Any ways 1) the system is in vacuum and<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">second while running it for quite long, minimization of energy will<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">automatically take place.</DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">You should probably start by doing the tutorial and browsing the web<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">site, check out the flow chart for doing simulations.</DIV> </BLOCKQUOTE><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; ">Erik Marklund, PhD Student, Molecular Biopcysics 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>75124 Uppsala, Sweden</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phone: +46 18 471 4537<SPAN class="Apple-converted-space"> </SPAN>fax: +46 18 511 755</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A></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; ">_______________________________________________</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></BODY></HTML>