AMBER Archive (2009)

Subject: [AMBER] 1-4 vdW, GB MM difference

From: Jimmy Heimdal (Jimmy.Heimdal_at_teokem.lu.se)
Date: Thu Apr 16 2009 - 06:57:01 CDT

Hi everyone

I try to calculate MM-(PB/GB)SA energies, and get a strange 1-4 vdW
energy difference between a GB and MM calculation.

Energies for GB.
  BOND = 166.9817 ANGLE = 685.7762 DIHED =
3438.4813
  VDWAALS = -3218.8913 EEL = -27411.0184 EGB =
-2741.2845
  1-4 VDW = 4830.2957 1-4 EEL = 18209.8251 RESTRAINT =
0.0000

Energies for MM.
  BOND = 166.9817 ANGLE = 685.7762 DIHED =
3438.4813
  VDWAALS = -3218.8913 EEL = -27411.0184 HBOND =
0.0000
  1-4 VDW = 1210.8295 1-4 EEL = 18209.8251 RESTRAINT =
0.0000

The result is the same with both amber 9 and 10. Is this a bug?
I attach prmtop prmcrd and input files for testing.

Thank you for your help.

Jimmy Heimdal
jimmy.heimdal_at_teokem.lu.se
tel +46462224915

pbsa file for QM/MM-PBSA PB calculation; from MM/PBSA, UR 5/12-08
  &cntrl
  ntf = 1, ntb = 0, dielc = 1.0,
  idecomp= 0,
  igb = 5, saltcon= 0.00,
  offset = 0.09,
  intdiel= 1.0, extdiel= 80.0,
  gbsa = 0, surften= 1.0,
  cut = 999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2
  imin = 1, maxcyc = 1, ncyc = 0,
 &end

pbsa file for QM/MM-PBSA PB calculation; from MM/PBSA, UR 5/12-08
  &cntrl
  ntf = 1, ntb = 0, dielc = 1.0,
  idecomp= 0,
  igb = 0, saltcon= 0.00,
  offset = 0.09,
  intdiel= 1.0, extdiel= 80.0,
  gbsa = 0, surften= 1.0,
  cut = 999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2
  imin = 1, maxcyc = 1, ncyc = 0,
 &end




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