[gmx-users] Question about gcc version

[Justin A. Lemkul]

> > 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
> >>> jalemkul at vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >>>
> >>> ========================================
> >>> _______________________________________________
> >>> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >>> 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.
> >> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> >> 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
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> 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
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================