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

[Szilárd Páll]

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.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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>