RE: AMBER: box size bomb in QMMM calculation

From: Ross Walker <>
Date: Tue, 12 Jun 2007 20:39:35 -0700

Hi Bud,

> > cut off unreasonably small for this, say 0.1 A just to
> force it to get to
> > the pdb writing stage.
> >
> That was my plan, but it never gets far enough to do that. It bombs
> before the QM region pdb write occurs.

Did you try setting cut=0.1? That should get you through to the pdb writing
phase, although obviously the actual MD will be garbage. Alternatively you
could try turning off periodic boundaries - set ntb=0, then it will skip the
cut off bounding check and you;ll get a pdb.

> Unfortunately, I'm leaving tomorrow morning to go to the US
> Grand Prix.

Wow, lucky for some... I just have to resign myself to watching it on Speed.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Wed Jun 13 2007 - 06:07:39 PDT
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