Hi Jason,
Force field is ff12SB. I now made sure that MMPBSA.py is the one from
AmberTools 13 (from the comment on the top: "Last updated: 12/03/2012")
- with the error message now appearing... I have %FLAG RADIUS_SET
(mbondi) and %FLAG RADII set in the parmtop though.
Cheers,
Hannes.
On Tue, 25 Jun 2013 07:59:08 -0400
Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Jun 25, 2013 at 6:05 AM, Hannes Loeffler
> <Hannes.Loeffler.stfc.ac.uk
> > wrote:
>
> > Hi,
> >
> > the atom types '2C', '3C', 'C8', 'CO' (and possibly others) seem to
> > be missing from sa_driver.F90. What radii would I need for those?
> > Alternatively, what atom types could I change them to?
> >
>
> What force field did they come from? The better approach IMO is to
> use an up-to-date AmberTools 13 that automatically uses the radii
> from the prmtop file instead of trying to determine its own from
> FF-specific atom types.
>
>
> > Note: MMPBSA.py only gave me a CalcError because mmpbsa_py_energy
> > had failed. But no details as to why. It would be good to have
> > the actual cause for the error. I had to figure out how to run
> > mmpbsa_py_energy before I knew what was going on.
> >
>
> This was actually addressed as bugfix.24 of AmberTools 12 [
> http://ambermd.org/bugfixesat.html], so I'm guessing the version you
> are using is out-of-date. Fully updating AmberTools 12 to the latest
> version (or even better, using AmberTools 13 full updated instead)
> would fix this.
>
> All the best,
> Jason
>
--
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Received on Tue Jun 25 2013 - 05:30:03 PDT
