Hi Chris and everyone,
The bug in question affects 5.0.x and it is related to the hackblock
handling of pdb2gmx. As the above linked redmine page indicates, it is
indeed a duplicate of previously reported issues (#1755 and #1755). It has
been first identified and fixed as a bug a few weeks ago, but having caught
the devs in the middle of vacation it has not been announced or included in
a release (except 5.1-RC1). Apologies for that.
Initial analysis on the effect of the bug on the AMBER99sb-ildn FF was that
2-3 sidechain torsions were roughly half-way between 99sb and 99sb-ildn.
Details will be published on the bug report page:
http://redmine.gromacs.org/issues/1755
Full details and full analysis will be provided soon with the 5.0.6 bugfix
release. The fix is the the development version and can be obtained by
building the release-5-0 branch from git.
Cheers,
--
Szilárd
On Wed, Jul 22, 2015 at 7:35 PM, Christopher Neale
chris.ne...@alum.utoronto.ca wrote:
Dear Users:
I believe that gromacs 5 pdb2gmx does not faithfully reproduce the
AMBER99sb-ILDN force field. I wanted to make a notice here so that people
who are using that combination can compare the topologies they get out of
gromacs 5 pdb2gmx to gromacs 4 pdb2gmx.
Details are here: http://redmine.gromacs.org/issues/1778
Thank you,
Chris.
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