AMBER Archive (2009)

Subject: [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out

From: Jeff Yeo (weekiang_at_live.com)
Date: Mon Oct 05 2009 - 18:22:53 CDT

Hi,
 
I am in the midst of running the binding energy calculations using the mm_pbsa.pl script. I checked on the snapshot_com.all.out and found that almost all entries have different missing values at different timepoints. They either have 'values' of NaN or Infinity or *********.
 
I doubt this is normal. What may be causing these weird 'values'? The generation of snapshots from mdcrd proceeded smoothly and the output file of this binding energy calculations did NOT contain any errors or warnings.

 
156
 BOND = ************* ANGLE = 441946.7100 DIHED = 15022.5337
 VDWAALS = ************* EEL = -5029.7507 EGB = -20626.4938
 1-4 VDW = NaN 1-4 EEL = Infinity RESTRAINT = 0.0000
 
157
 BOND = ************* ANGLE = 465389.2004 DIHED = 14791.2394
 VDWAALS = 32227929.3027 EEL = -3444.9296 EGB = -21619.6342
 1-4 VDW = 16964395.6854 1-4 EEL = -2484.8846 RESTRAINT = 0.0000

158
 BOND = ************* ANGLE = 505512.7190 DIHED = 14019.5864
 VDWAALS = ************* EEL = -1393.7833 EGB = -41493.6393
 1-4 VDW = ************* 1-4 EEL = -448.3567 RESTRAINT = 0.0000

159
 BOND = ************* ANGLE = 512063.7966 DIHED = 14958.8929
 VDWAALS = ************* EEL = -1367.3170 EGB = -40169.3247
 1-4 VDW = ************* 1-4 EEL = -183.7412 RESTRAINT = 0.0000
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