Use the -mk flag for antechamber - see Amber 8 manual page 79.
E.g for the sustiva test case you would use:
antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prep -c bcc -s 2
-mk "LBFGS"
Note, in the limited trial I just tried the divcon.in file that was created
by antechamber did not have any of the defaults options in it, only the
LBFGS option. Hence I think you need to put all the options in the -mk "
"'s. I.e -mk "CARTESIAN AM1 STANDARD DIRECT OPT=LBFGS XTEST=0.0001"
(Don't specify the charge flag here though..)
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Kennie Merz
Sent: 14 July 2004 10:04
To: steven.j.enoch.gsk.com
Cc: amber.scripps.edu
Subject: Re: AMBER: Problem with divcon - increasing MXATTS?
Hi,
You need to find where the keywords are defined for AnteChamber. For the
QM/MM code they are in the keyword file, but for Antechamber I am not sure.
Anyone on the list know how to change the keywords for DivConLite in
AnteChamber? LBFGS is a limited memory BFGS and works quite well and avoids
the MXATTS problem. Kennie
On Jul 14, 2004, at 12:45 PM, steven.j.enoch.gsk.com wrote:
Kennie,
I don't quite understand how I implement the 'OPT=LBFGS' option, if you
could explain to me how to use it I would be very grateful!
Many Thanks
Dr Steve Enoch
GlaxoSmithKline
UK
Professor Kenneth M. Merz, Jr.
152 Davey Laboratory
Department of Chemistry
The Pennsylvania State University
University Park, Pennsylvania 16802
e-mail: merz.psu.edu
http: http://merz.chem.psu.edu
QBio DB: http://qbiodb.chem.psu.edu
Phone: 814-865-3623
FAX: 814-863-8403
Cell: 814-360-0376
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Received on Wed Jul 14 2004 - 19:53:00 PDT
