[pavan.bnpi.com: 'Coordinate resetting in amber6']

From: David Case <case_at_scripps.edu>
Date: Wed 17 May 2000 15:08:18 -0700

----- Forwarded message from Pavankumar Petluru <pavan_at_bnpi.com> -----

Date: Wed, 17 May 2000 13:41:50 -0500
From: Pavankumar Petluru <pavan_at_bnpi.com>
Organization: BioNumerik
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To: case_at_scripps.edu
Subject: 'Coordinate resetting in amber6'

Dear Prof. Case,

We are trying to mutate a drug molecule in the presence of
DNA and solvent water (using GIBBS). To prepare the system,
we followed the tutorial on DNA (AMBER website) like

(1) Simple minimization with DNA constrained (with a force
of 20 kcal on DNA)
(2) MD with DNA constrained (with a force of 500 kcal on DNA)
for 25 ps
(3) MD with PME with DNA constrianed (with a force of 500 kcal
on DNA) for 25 ps
(4) Simple minimization with DNA constrined (with a force of
25 kcal on DNA)
(5) MD with PME but no constraints for 3ps
(6) took the restart from Step 5 and started 'gibbs' and the job
terminates with 'volume of ucell too big' a regular restart should
fix things.

What is meant by regular restart. In the above gibbs job we manually
turned off SHAKE.
When we make NTC=3, the gibbs job terminates with
'Coordinate Resetting Error'

Could you please let me know if there is any way we can circumvent
these problems. We are using Box option, and Xleap added the Na+ ions
by using the 'addions' command. We have a total of 13200 atoms
including the DNA,ions, and solvent water.

Thank you very much for your help.


Dr. Pavankumar Petluru
Application Scientist
BioNumerik Pharmaceuticals
8122 Datapoint Drive
Suite 1250
San Antonio, TX 78229
phone: 210-614-1701 x 232 (office)
phone: 210-408-0549       (home)
fax  : 210-615-8030
email: pavan_at_bnpi.com
----- End forwarded message -----
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.         |  WWW:                         
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
Received on Wed May 17 2000 - 15:08:18 PDT
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