Thank you Jason for the response. We dont have that Amber15 but can upgrade
to Ambertools13. Do you think that can work?
Regards
On Wed, Jul 22, 2015 at 12:23 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Jul 21, 2015 at 12:55 AM, Ayesha Fatima <ayeshafatima.69.gmail.com
> >
> wrote:
>
> > Dear All,
> > I have run 2ns qm/mm on a stabilised ligand-protein complex using
> AMBER12.
>
> I want to calculate the free binding energy. First I used the mm_pbsa.pl
> > using the script by Holger Gohlke. I modified the &GB section to include
> > the qm parameters. The output returned positive values for GBTOT which
> are
> > rather high.
> > Then I tried to use the mmpbsa.py method and created the mmpbsa.in file
> as
> > indicated on the mailing list. The mdins files were created and as
> > mentioned on the mailing list to remove the "dec_verbose" and rerun the
> > mmpbsa. I did that however the error of CalcError: sander failed with
> > prmtop ../prot33.top! is coming.
> > Can someone guide me to set up?
> >
>
> Do you get the same issue when you run with AmberTools 15? Amber 12 is
> rather old at this point (released over 3 years ago), and there have been
> numerous fixes and improvements to MMPBSA.py since then.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 21 2015 - 18:30:02 PDT
