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
>
>
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Received on Wed Jun 11 2014 - 09:30:02 PDT
