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using is out-of-date.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
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 25 2013 - 05:00:06 PDT
