Justin A. Lemkul wrote:
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.
If it works it works, but anyone using a Mac has gcc-4.0.x (including
me). Mixing of packages could be an explanation.
--
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
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