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: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue Nov 12 2002 - 06:06:47 PST
