Re: [gmx-users] Hi..

[Navratna Vajpai]

Many thanks Eric, it worked. I didn't really had look into this. Best regards Nav On Aug 16, 2006, at 11:34 AM, Erik Marklund wrote: On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote: Navratna Vajpai wrote: Hey Mark.. I had attached the file along with the mail. I think you could  not receive it. let me paste the contents and explain it little more.  I am trying to run the simulation in vacuum of a nona peptide. I managed  to get pdb2gmx working and even further the EM working. But when I tried  to do the MD run after a small minimization of protein, I got an error  message after the execution of grompp. The execution asked for the -n  option which indicates for the index file. 1) I don't know why it asked for? My guess it's because of this line in the mdp file: tc-grps     =  protein      sol Apparently you have temperature-coupled the solvent, even though you have no solvent. Vacuum, right? Note that grompp is looking for 'sol' and, when it can't find it among the default groups (see manual), it looks for an index file: Fatal error: Group sol not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Try removing 'sol' from the mdp file. If you are simulating in vacuum, you (probably) have no solvent. /Erik 2) If it ask for is there any way to solv this problem. Actually i tried  using that also. But the error stayed back.  I am also pasting the error after the grompp. Somehow this could not  prepare the input file for the MD run.  3) third question is: I am wondering whether i can start my run just  after the execution of pdb2gmx. Any ways 1) the system is in vacuum and  second while running it for quite long, minimization of energy will  automatically take place. You should probably start by doing the tutorial and browsing the web  site, check out the flow chart for doing simulations. --  Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,          75124 Uppsala, Sweden phone: +46 18 471 4537          fax: +46 18 511 755 [EMAIL PROTECTED] _______________________________________________ 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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