[AMBER] Sander Error

From: Melissa Buskes <M.Buskes.latrobe.edu.au>
Date: Tue, 8 May 2012 05:27:40 +0000

Hello,

I am currently attempting to run a minimisation of a complex (Inhibitor and protein) using Sander. I have been having problems running this on AMBER 11 with the following output files displaying this "error":

| Local SIZE OF NONBOND LIST = 4301123
| TOTAL SIZE OF NONBOND LIST = 16457817


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -Infinity NaN 1.7578E+06 O 1901

 BOND = 1086.8743 ANGLE = 2985.4907 DIHED = 3754.6339
 VDWAALS = 214218.6554 EEL = -113699.4160 HBOND = 0.0000
 1-4 VDW = -Infinity 1-4 EEL = -Infinity RESTRAINT = 0.0000

I then resubmitted the jobs on AMBER 10 and the jobs appeared to run fine. This is the same component of the output file:

 Local SIZE OF NONBOND LIST = 4299672
| TOTAL SIZE OF NONBOND LIST = 16453545


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 9.1094E+05 5.2338E+04 1.1077E+07 HB3 1874

 BOND = 1086.8743 ANGLE = 2985.4907 DIHED = 3754.6340
 VDWAALS = 1000086.7124 EEL = -113709.9625 HBOND = 0.0000
 1-4 VDW = 1382.9392 1-4 EEL = 15352.7435 RESTRAINT = 0.0000

Is there maybe something that I have overlooked in regards to differences between AMBER 10 and 11? As I am using the exact same input files in both cases.

Initially, I thought this result may have been an issue with clashing atoms, but I have since checked and resolved that these do not exist anymore.

Any help/ suggestions would be much appreciated,

Thank you,

Melissa













---------------------------------------------
Melissa Buskes
PhD student
Department of Chemistry | School of Molecular Science
La Trobe University
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Received on Mon May 07 2012 - 22:30:03 PDT
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