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 - 10:30:03 PDT
