Re: problem in PME

From: David A. Case <>
Date: Tue 12 Nov 2002 06:06:47 -0800

On Tue, Nov 12, 2002, Monica wrote:

> I am running DRU-DNA complex on AMBER6 in vacuum....

> My input file is:
> B&cntrl
> imin=1, ncyc=50, maxcyc=1000, nmropt=1, cut=8.0,
> ntpr=100, ntb=1, scee=1.2, ntr=1, scee=1.2
> &end

Setting ntb=1 implies you have a periodic simulation, not a vacuum. My
recollection was that we also recommended using sander_classic for vacuum
calculations in Amber 6. You can get things to work in sander (check the
instructions or the mail archives carefully), but this was less efficient
than running the calculation with sander_classic.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Tue Nov 12 2002 - 06:06:47 PST
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