AMBER Archive (2009)

Subject: [AMBER] pupil and amber

From: davide branduardi (davide.branduardi_at_gmail.com)
Date: Tue Dec 22 2009 - 14:29:37 CST

Dear All,
I'm trying to use AMBER10 together with PUPIL to do a qmmm calculation.
The setup of amber10 (bugfixed with the latest patch) with make sander.PUPIL
works fine and the setup of pupil runs fine as well.
Unfortunately when I run the tests (ala3 with g03)
I got some problems specifically connected with the amber code
The line that pupil call is

./sanderLinux -O -i mdin -p ala3.parm7 -c ala3.inpcrd -ORBInitialPort 3001
-ORBInitialHost baldios -OptPrint 5 -jxms 64 -jxmx 4096 -jxss 16

(where sanderLinux is a link to sander.PUPIL )
but sander ends up with an error which is

     mdfil: Error unknown flag: -jxms

     usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
-radii radii -y inptraj]
Consult the manual for additional options.

In fact mdfil.f (After being patched with pupil) routine does contain
ORBInitialPort -ORBInitialHost -OptPrint options but not -jxms
-jxmx -jxss.
I suspect that these are connected with CORBA and this make me think that
probably my java installation or the runtime
environment is not properly set.
Anyone can help me?
Best regards

Davide 

-- 
**************************************************************
Davide Branduardi
Post Doc- Computational Chemistry
Drug Discovery and Development
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
Phone: +39 010 71781573              Room: 1/27
Fax:   +39 010 7170187

e-mail:
davide.branduardi_at_iit.it
davide.branduardi_at_gmail.com
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