AMBER Archive (2008)

Subject: AMBER: SANDER BOMB in subroutine nonbond_list

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Wed Jan 30 2008 - 09:13:45 CST

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

 

Pankaj

 

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

 


  • application/octet-stream attachment: eqlb3.out

  • application/octet-stream attachment: eqlb3.in

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