> > Thanks David. I ran the test set, and got the following: > > > > $ ./gmxtest.pl all > > No topol.tpr file in morse. grompp failed > > FAILED. Check files in morse > > 1 out of 16 simple tests FAILED > > FAILED. Check files in dec+water > > 1 out of 14 complex tests FAILED > > All 63 kernel tests PASSED > > Error not all 45 pdb2gmx tests have been done successfully > > Only 38 energies in the log file > > > > For the "No topol.tpr file in morse" error, the grompp.out file shows: > > > > Fatal error: > > number of coordinates in coordinate file (conf.gro, 1490) > > does not match topology (topol.top, 0) > > > > ...although I'm not sure why. > Look further up in the grompp.out file >
Alright, I tracked this one down to the fact that the "include" line was pointing to a non-existent directory (/home/gmx/top). I changed that in the grompp.mdp and all is well. > > > > > The dec+water failure has been discussed before, although the discrepancy > is > > slightly different than that listed on the wiki: > > > > There are 5 terms to compare in the energy files > > > > LJ (SR) step 34: -0.21167, step 34: -0.171631 > > > > The pdb2gmx.log file shows that there is some discrepancy in the .mdp > > parameters: > > > > WARNING 1 [file ../../../../em.mdp, line unknown]: > > Unknown left-hand 'bd-temp' in parameter file > > > > checking input for internal consistency... > > processing coordinates... > > > > ------------------------------------------------------- > > Program grompp, VERSION 3.3.3 > > Source code file: futil.c, line: 345 > > > > File input/output error: > > b4em.gro > > ------------------------------------------------------- > > > > I'm guessing this is just a reflection of changes that have been made > between > > versions 3.3.2 and 3.3.3? But I don't know what to make of the "38 > energies in > > log file." Is there some more relevant output I can post to help clarify > the > > situation? > Again, here you may need to look more closely in the output file. If > b4em.gro does not exist something went wrong before. > This error seemed a bit more worrisome. It turns out that the initial pdb2gmx conversion to conf.gro failed, giving a similar error to one that I reported in a bugzilla not too long ago (http://bugzilla.gromacs.org/show_bug.cgi?id=171). This time around, pdb2gmx complained: Fatal error: Atom H not found in residue 2 while adding improper It turned out that (in the bug report) the Gromacs installation was from a broken Ubuntu package on that particular machine. Looks like using gcc 4.0.1 might result in a similarly broken package in this case. I have installed gcc-3.3, used it to re-compile Gromacs 3.3.3, and all the tests pass except for the dec+water, which seems OK to me. -Justin > > > > > > Thanks, > > Justin > > > >>> Thanks for any insights. > >>> > >>> -Justin > >>> > >>> > >>> ======================================== > >>> > >>> Justin A. Lemkul > >>> Graduate Research Assistant > >>> Department of Biochemistry > >>> Virginia Tech > >>> Blacksburg, VA > >>> [EMAIL PROTECTED] | (540) 231-9080 > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > >>> > >>> ======================================== > >>> _______________________________________________ > >>> gmx-users mailing list gmx-users@gromacs.org > >>> 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 gmx-users@gromacs.org > >> 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 > >> > > > > > > > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > [EMAIL PROTECTED] | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > 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. > ________________________________________________________________________ > 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 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
