thanks a lot for such clear explanations.
I noticed that I have specify the receptor charge explicitly otherwise
it would be some problem for mmpbsa.py to get the correct values.
BTW, does the latest amber support QM/PBSA now?
thx again.
On 07/22/2015 01:38 PM, Jason Swails wrote:
> This says that the 9th CPU (first CPU is rank 0) failed when trying to
> compute the QM/MM-GBSA energy with the complex topology file. This is
> *all* that the above error message states. The error message generated by
> sander will have been placed inside the _MMPSBA_complex_gb.mdout.8 file.
> The error message there will hopefully give you more information that will
> help solve the problem.
>
> One word of warning is that picking a QM region is difficult if you plan on
> allowing bonds to cross the QM-MM boundary. The standard choices allowed
> by MMPBSA.py may be inadequate when it comes to picking the QM region, as
> it only allows you to pick residues that will be treated with QM. For
> protein systems, this will mean that amide bonds -- which are conjugated pi
> systems -- will be cut along the QM-MM boundary, which might lead to
> difficulties in converging the QM/MM SCF.
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Received on Wed Jul 22 2015 - 07:30:02 PDT
