Hi All,
I just grabbed the latest version of the test set from CVS, noting the updates
and improvements to the package. I ran gmxtest.pl, and all simple, complex, and
kernel tests passed, but pdb2gmx failed. Looking into the pdb2gmx.log file,
grompp complains about "Unknown or double left-hand 'bd-temp' in parameter
file." Commenting this line out in the em.mdp file circumvents the problem, but
leads to multiple failures of the ffoplsaa+tip4p/tip5p (-vsite none) tests
involving the 1pga.pdb structure. The problem is naming inconsistency between
MW-HW3 in the case of tip4p, and LP1/LP2-HW3/HW4 in the case of tip5p. Of
course, these errors come from pdb2gmx processing of the crystal waters and use
of the hydrogen database.
To circumvent all of these problems in one move, I made the following change to
the gmxtest.pl script:
355c355
< open(PIPE,"$grompp -f ../../../../em -c b4em 2>&1 |");
---
> open(PIPE,"$grompp -maxwarn 10 -f ../../../../em -c b4em 2>&1
|");
Perhaps this change would be appropriate for the general public as well. With
this modification, every test passes as expected, since grompp will correctly
use the names from the topology.
It might also be appropriate to kill the bd-temp line in em.mdp, since this is
not a valid .mdp option any more :)
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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