Thank You Jason for the email. I will try and see what happens.
Thank you again
Ayesha Fatima
UM
On Fri, Apr 22, 2016 at 1:02 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Apr 21, 2016 at 11:32 AM, Ayesha Fatima <ayeshafatima.69.gmail.com
> >
> wrote:
>
> > Dear All
> > I want to run the MMPBSA.py calculation for my QM/MM simulations. I am
> > having a small issue while running this calculation. below is my input
> file
> >
> > &general
> > startframe=1, endframe=1000, interval=100, verbose=2, keep_file=0,
> > use_sander=1
> > /
> > &gb
> > igb=5, saltcon=0.100,
> > ifqnt=1, qm_residues="211,249,252,281,545,546,568", qmcharge_lig=0,
> > qmcharge_rec=-1, qmcharge_com=-1,
> > qm_theory="PM6"
> > /
> >
> > Previously I ran this file a few months ago and ran without any problem.
> > However now it gives me the error of
> >
> > You most likely have the charge of : System specified with odd number of
> > electrons ( 427) but odd spin ( 1). ) QM region (qmcharge) set
> > incorrectly
> >
> > I have checked the charges in Gaussian and I get 0 charges on complex,
> > ligand and receptor but receptor and complex are doublets while ligand is
> > singlet.
> >
> > I ran the same parameters in MMPBSA.pl and it is not showing any problem.
> >
> > because of this AMBER is showing the calculation error with water
> stripped
> > complex file. Also the same old issue of the mdins disappearing once I
> use
> > the -use-mdins command.
> >
> > I am using AMBER 12 and AMBER TOOLS 13.
> >
>
> ​Make sure you apply all updates and try again. There was a bug in
> AmberTools 13 where the charge was always set to 0 (see update.19 for
> AmberTools 13: http://ambermd.org/bugfixes/AmberTools/13.0/update.19).
>
> However, I would suggest upgrading to AmberTools 15, since a few other
> issues have been fixed since then, as well.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Thu Apr 21 2016 - 19:30:05 PDT
