Re: [AMBER] QM/GBSA calculation failed

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 22 Jul 2015 10:31:00 -0400

> On Jul 22, 2015, at 10:24 AM, Albert <mailmd2011.gmail.com> wrote:
>
> 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?

No. And that is not in the plans as far as I know.


>
> thx again.
>
>
>> On 07/22/2015 01:38 PM, Jason Swails wrote:
>> ‚ÄčThis 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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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 22 2015 - 08:00:02 PDT
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