AMBER: SANDER BOMB in subroutine nonbond_list

From: Pankaj R. Daga <>
Date: Wed, 30 Jan 2008 09:13:45 -0600

Dear Amber Community


Thanks for your suggestions about setting up the input file for the QM/MM
simulation. As suggested by Dr. Case, I have decreased the number of atoms
in QM region from 110 to 67. The input file works fine.


I have carried out minimization, heating and initial equilibration using MM
method. Now, I intend to carry out equilibration using QM/MM integration. I
am facing new error in the simulation. The job starts and gets aborted after
20 minutes with the error message,


"SANDER BOMB in subroutine nonbond_list

  volume of ucell too big, too many subcells

  list grid memory needs to be reallocated, restart sander"


I have searched in the archives for similar error, I could not succeed.
Could anyone please suggest me the reason for this error? I would appreciate
if you please can suggest me a way out. I am attaching my input and output
file along with.


Thanks and Regards




If your ship doesn't come in, swim out to it...Jonathan Winters
Pankaj R. Daga |
Dept. of Medicinal Chemistry | e-mail:
417 Faser Hall, | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Sun Feb 03 2008 - 06:07:07 PST
Custom Search