Hello,
I am repeating the amber tutorial A9 (Ħħ Small molecule binding to
T4-lysozyme L99AĦħ). I am confused about the output energy terms of the
step 2, changing uncharged benzene to uncharged phenol. The output of
amber11 are below.
DV/DL, AVERAGES OVER 100000 STEPS
NSTEP = 100000 TIME(PS) = 250.000 TEMP(K) = 0.01 PRESS = 0.0
Etot = 0.6223 EKtot = 0.6223 EPtot = 2.6136
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = -8.1255 VDWAALS = -3.4072
EELEC = 14.1463 EHBOND = 0.0000 RESTRAINT = 0.0000
DV/DL = 2.6136
Ewald error estimate: 0.3317E-08
You can see that there are three terms contribute to the DV/DL, they
are 1-4 EEL = -8.1255, EELEC = 14.1463, VDWAALS = -3.4072. am I right?
In this step 2, I only changed the uncharged BNZ to uncharged PHN,
which was beside the charge question. I think the DV/DL should be
equal to the VDWAALS terms. However,
DV/DL = VDWAALS + 1-4EEL + EELEC, which including the total
electrostatic energy!
I wonder am I wrong? Why?
Best regards
Dandan
Nanjing University, China.
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Received on Wed Sep 04 2013 - 18:30:02 PDT
