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