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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 08 2012 - 16:30:03 PDT
