Hi Blaise, Disulfide bonds are only made when two Cys-S atoms are within 0.2 +/- 0.02nm from each other. This distance is in the file specbond.dat. You can search the archives for how to make the bond.
Also, please start a new thread rather than replying to a message. Now there's debris unrelated to your question, which is a bit annoying. Cheers, Tsjerk On Nov 30, 2007 12:41 AM, Blaise Costa <[EMAIL PROTECTED]> wrote: > Hello Gromacs users, > I have docked an antagonist into the agonist bound conformation and doing > MDS to get the antagonist bound conformation after several nS simulation. > Therefore expected that the protein might undergo big conformational > changes, and running the simulation in "Unconstrained Start = Yes" . While > starting the simulation the S atoms were close enough (3A<) to make the > disulphide bond. Now, after 1.5 nS, noticed that it is deviated for more > than 6.5A, therefore no way to make the bond. Is there any way that I can > give constraint for these bonds and can I restart the program from last > point? > > I gave -SS command during pdb2gmx, believed that gromacs will keep the S > atoms close enough to make the S-S bond. I am using Gromacs version 3.3.1! > > Many thanks in advance! > > Blaise > > > ----- Original Message ---- > From: David van der Spoel <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > Sent: Thursday, November 29, 2007 12:29:57 PM > Subject: Re: [gmx-users] Double precision test failure > > Chris Snook wrote: > > I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHzCore 2 > > Duo processor. > > > > I have downloaded and installed the v 3.3.2 binaries of gromacs for this > OS and > > run the test program. The single precision tests run OK. But the double > > precision tests completely fail with the following output (partial): > > > > No topol.tpr file in angles1. grompp failed > > FAILED. Check files in angles1 > > No topol.tpr file in angles125. grompp failed > > FAILED. Check files in angles125 > > No topol.tpr file in bham. grompp failed > > FAILED. Check files in bham > > etc > > No topol.tpr file in kernel334. grompp failed > > FAILED. Check files in kernel334 > > 63 out of 63 kernel tests FAILED > > readline() on closed filehandle PIPE at ./gmxtest.pl line 353. > > etc > > > > I've checked the archives and the manual and haven't seen anything > relevant to > > this. Any help would be appreciated. > > did you source GMXRC? > > > > Regards > > > > Chris > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > > ------------------------------ > Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try > it > now.<http://us.rd.yahoo.com/evt=51731/*http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ%0A> > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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