[gmx-users] gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field

Szilárd Páll pall.szilard at gmail.com
Wed Jul 22 22:39:03 CEST 2015

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:

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.



On Wed, Jul 22, 2015 at 7:35 PM, Christopher Neale <
chris.neale at 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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