AMBER Archive (2007)

Subject: AMBER: Minimization increases energy

From: Hayden Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Wed May 23 2007 - 11:21:35 CDT

 
Dear Amber users

I have taken an NMR structure of a small protein and minimized it with
sander in implicit solvent (igb=1). My output is as follows:

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -3.6789E+02 1.7668E+01 1.8766E+02 O 334

 BOND = 65.9631 ANGLE = 61.8355 DIHED =
298.1987
 VDWAALS = 44.4613 EEL = -2385.5904 EGB =
-739.8229
 1-4 VDW = 198.2850 1-4 EEL = 2088.7822 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
   1000 -8.8062E+02 7.4882E-02 5.1163E-01 C 529

 BOND = 18.6956 ANGLE = 61.2032 DIHED =
256.7138
 VDWAALS = -223.5801 EEL = -2398.7351 EGB =
-729.0717
 1-4 VDW = 101.0093 1-4 EEL = 2033.1486 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
   2000 -8.9380E+02 1.0086E-01 6.8560E-01 CE1 393

 BOND = 18.8494 ANGLE = 61.0641 DIHED =
252.0533
 VDWAALS = -228.2521 EEL = -2407.6584 EGB =
-728.9162
 1-4 VDW = 102.8656 1-4 EEL = 2036.1992 RESTRAINT =
0.0000

  etc etc with increasing energy, which then eventually begins to decrease
again.

Does anyone out there know why I have such a drastic energy increase when I
only expect ever to see a decrease?

My sander input file is:

 minimization with sander (Amber9)
 &cntrl
  imin = 1, maxcyc = 50000, drms = 0.005, ntb = 0,
  ntpr = 1000, cut = 80., igb = 1, rgbmax = 40, ncyc = 100
 &end

Many thanks in advance

Hayden Eastwood

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu