The error seems rather straightforward and beyond what we can answer
without seeing your exact qmmask selection. Can you double check the charge
and number of electrons that should be (or you expect) on your quantum
regions? Does your ligand include any metal centers?
Regards,
Brian
On Wed, Jun 11, 2014 at 12:01 PM, John Smith <ddfd09.gmail.com> wrote:
> Hi Jason,
>
> Thank you so much for your email. I was able to start the QM/MM-GBSA and
> the process started OK by calculating the contribution from the complex but
> stopped once it got the the receptor stage with an error messege of failure
> with the receptro prmtop file. The QM region in my system includes a
> deprotonated cysteine residue (CYM123) and a positively charged ligand
> numbered 432. I set the charges in the input file as follows:
>
> qmcharge_com=0, qmcharge_lig=1, qmcharge_rec=-1
>
> The out file (_MMPBSA_receptor_gb.mdout) of the receptor from QM/MM-GBSA
> states at the end:
>
> QMMM: System specified with odd number of electrons ( 35)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> calculation.
>
> Could you please tell me how do I need to set the charges?
>
> Many thanks,
> Mahmood
>
>
>
>
> On 11 June 2014 13:35, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Wed, 2014-06-11 at 12:31 +0100, John Smith wrote:
> > > Hi AMBER users,
> > >
> > > Could you please help me with the command for running QM based binding
> > > energy calculation. I have a prmtop file for the solavted complex, a
> > prmtop
> > > file for the complex, a prmtop file for the protein on its own and the
> > > ligand on its own. The iput file I am using is:
> > >
> > > &general
> > > startframe=1, endframe=200, interval=5,
> > > ifqnt=1, qmcharge=0, qm_residues='123, 432'
> > > qm_theory='PM3', qmcharge_lig=1, qmcharge_rec=-1
> > > /
> > > &gb
> > > igb=5, saltcon=0.100,
> > > /
> > >
> > > I know that it requires a *sander *functionality but I could not
> > implement
> > > this into the command.
> >
> > MMPBSA.py will automatically use sander when it needs to (such as when
> > you are using QM/MM-GBSA). You don't have to _do_ anything else special
> > in your input file.
> >
> > In the past, sander was released as part of Amber (not AmberTools), and
> > so you needed a paid license to run QM/MM-GBSA calculations (or anything
> > else requiring sander) -- that is why the distinction was made. This is
> > no longer the case.
> >
> > >
> > > I am also trying to run nmode binding energy calculation using the same
> > > prmtop files mentioned above and the following inout file:
> > >
> > > &general
> > > endframe=200, keep_files=2,
> > > /
> > > &nmode
> > > nmstartframe=1, nmendframe=200,
> > > nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> > > /
> > >
> > > The calculation takes hours and then stops recording an error in the
> > prmtop
> > > file for the non-solvated complex. I have used these exact prmtop file
> to
> > > run ordinary GB and PB free energy calculations and they are working
> fine
> > > for me.
> >
> > Try Googling the exact error message you get. My guess is that someone
> > else has seen this problem before and there will be old threads that
> > tell you the problem.
> >
> > We cannot help when all we know is "something did not work". We need
> > output, error messages, and input (copy-and-paste, do not paraphrase).
> >
> > 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
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
====================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 11 2014 - 09:30:03 PDT
