From: Jason Swails <>
Date: Wed, 11 Jun 2014 12:32:02 -0400

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 made a mistake writing the input files. From the information
you gave I don't know which one it is.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jun 11 2014 - 10:00:02 PDT
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