Re: [AMBER] QM/MMPBSA

From: John Smith <ddfd09.gmail.com>
Date: Wed, 11 Jun 2014 17:53:15 +0100

Hi Jason,

Thanks for the reply. I checked the files and there seems to be nothing
wrong. They are attached to the email along with PDB files for the protein
and the ligand


On 11 June 2014 17:32, Jason Swails <jason.swails.gmail.com> wrote:

> On Wed, 2014-06-11 at 17:01 +0100, John Smith 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?
>
> They need to be set correctly. Check the _MMPBSA_gb_qmmm_com.mdin,
> _MMPBSA_gb_qmmm_rec.mdin, and _MMPBSA_gb_qmmm_lig.mdin and make sure
> that the input looks correct.
>
> Either you made a mistake about what residues you really selected or
> MMPBSA.py made a mistake writing the input files. From the information
> you gave I don't know which one it is.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>


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Received on Wed Jun 11 2014 - 10:00:02 PDT
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