On Wed, 2014-06-11 at 17:53 +0100, John Smith wrote:
> Hi Jason,
>
> Thanks for the reply. I checked the files and there seems to be nothing
> wrong. They are attached to the email along with PDB files for the protein
> and the ligand
The problem is that MMPBSA.py is not printing the qm_charge to the input
file, so sander just assumes all QM regions have a neutral charge.
This bug was fixed in October of last year as the 19th and 20th updates
to AmberTools 13. See
http://ambermd.org/bugfixesat.html. Please make
sure you update to at least this version and compile that new version.
I suggest updating to AmberTools 14.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 11 2014 - 10:30:02 PDT
