AMBER Archive (2006)

Subject: AMBER: bad atom type: Li

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Thu Sep 21 2006 - 05:30:24 CDT

Dear amber users,

I have a problem on the system of multiple chain of polymer (PEO,PEI).
Also,these polymer is including Li+ and ClO-. Surprisingly, when i do leap
and then run sander in amber9 i found that this error below;

[vannajan_at_localhost peo8pei32li20clo20]$ sander -O -i gb_min_nueng.in -o
peo8nobox_testgb1.out -p peo8n.top -c testnoBox.crd -r peo8nobox_testgb1.rst
-x peo8nobix_testgb1.traj &
[1] 9644
[vannajan_at_localhost peo8pei32li20clo20]$ bad atom type: Li
[1]+ Exit 1 sander -O -i gb_min_nueng.in -o peo8nobox_testgb1.out -p
peo8n.top -c testnoBox.crd -r peo8nobox_testgb1.rst -x peo8nobix_

when take a look in output file i saw the command stop at this line below;
Energy minimization:
maxcyc = 100, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010

But, I don't know why amber can not recognite the Li+ atom so if anyone can
give me any suggestions I will appreciate.

Thanks a lot,

Jitrayut Jitonnom, Ph.D.(candidate)
Dept. of Chemistry,
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Tel: +66(0)6613-4218
Email: jitrayut.018_at_gmail.com <shafinaz_at_bri.nrc.ca>

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