AMBER Archive (2007)

Subject: AMBER: nucleic acid electrostatic energy

From: Tiago Sobreira (tiagojps_at_gmail.com)
Date: Sat Aug 04 2007 - 08:45:46 CDT

Hello Amber user,

I did the Amber tutorial *"Simulating a DNA polyA-polyT Decamer" *and
everything works fine. I tried to did little different things and change the
polyA-polyT DNA to a PolyG-polyC DNA and everything works fine too, but I
looked at the Amber output and I saw the electrostatic energy (EELEC) was
positive when the polyA-polyT DNA was negative.
I made a test, I created 4 pdbs files with only one base, one with base G,
one with base C, one with base A and one with base T. They were submitted to
a small minimization (500 steps) and a small dynamics (50000 steps) both
with IGB = 1. The result of the dynamics output was below:

Base G:
     A V E R A G E S O V E R 50000 S T E P S
 NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 306.85 PRESS =
0.0
 Etot = -129.7017 EKtot = 31.0986 EPtot = -
160.8003
 BOND = 13.6917 ANGLE = 18.1629 DIHED =
14.4233
 1-4 NB = 6.5796 1-4 EEL = -155.8129 VDWAALS = -
5.3587
 EELEC = 29.5956 EGB = - 82.0817 RESTRAINT =
0.0000
 ------------------------------------------------------------------------------

Base C:
     A V E R A G E S O V E R 50000 S T E P S
 NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 293.20 PRESS =
0.0
 Etot = -167.9384 EKtot = 27.0933 EPtot = -
195.0316
 BOND = 12.2789 ANGLE = 16.5758 DIHED =
16.7108
 1-4 NB = 7.8531 1-4 EEL = -215.1739 VDWAALS = -
3.7382
 EELEC = 46.0897 EGB = -75.6278 RESTRAINT =
0.0000
 ------------------------------------------------------------------------------

Base A:
     A V E R A G E S O V E R 50000 S T E P S
 NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 299.02 PRESS =
0.0
 Etot = -82.3565 EKtot = 29.4135 EPtot = -
111.7700
 BOND = 12.1006 ANGLE = 17.6828 DIHED =
15.3456
 1-4 NB = 7.6923 1-4 EEL = -44.1416 VDWAALS = -
4.4518
 EELEC = -37.3067 EGB = - 78.6912 RESTRAINT =
0.0000
 ------------------------------------------------------------------------------

Base T:
     A V E R A G E S O V E R 50000 S T E P S
 NSTEP = 50000 TIME(PS) = 50.000 TEMP(K) = 291.43 PRESS =
0.0
 Etot = -44.2100 EKtot = 28.6666 EPtot = -
72.8765
 BOND = 12.0543 ANGLE = 16.0767 DIHED =
16.1992
 1-4 NB = 7.3650 1-4 EEL = 16.4631 VDWAALS = -
4.0172
 EELEC = -68.5528 EGB = -68.4649 RESTRAINT =
0.0000
 ------------------------------------------------------------------------------

For Base A and T the EELEC was negative and Base G and C was positive. Any
one has any idea why this happeed?

Thanks
Tiago Sobreira

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