Hello
I posted this question along with another one last week, but since I
only got answers on one of my questions I'm reposting this question in
hope that somebody could help me.
I want to calculate the absolute dG of benzene to T4-lysozyme using TI
in Amber 10. I will follow the work by Roux, as cited in the Amber
manual (JCTC 2 p1255). This means that I want to add a restraint to my
benzene molecule. The restraint energy should not be included in the
dv/dl energies so I set dvdl_norest to 1. Now I have run a few lambdas
on the van der Waals-part, i.e. perturbing an uncharged benzene to
nothing but I'm confused about the output of sander. Here is a part of
the output for one of the lambdas
DV/DL, AVERAGES OVER 100000 STEPS
NSTEP = 100000 TIME(PS) = 320.000 TEMP(K) = -0.17 PRESS = 0.0
Etot = -8.9561 EKtot = -8.9561 EPtot = -22.2126
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 8.8226
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = -31.0353
EAMBER (non-restraint) = 8.8226
DV/DL = -53.2479
In a usual TI run, without restraint the EPTot is equal to DVDL, as
EPTot = V1-V0. But EPtot is also, in this case, VDWAALS+RESTRAINT as
it should be. But then I see that DV/DL, in this case is
EPtot+RESTRAINT=VDWAALS+2*RESTRAINT, although I do NOT want to include
the restraint energy in the dv/dl energy. In my book, if the only
thing I'm perturbing is the van der Waals-energy, the dv/dl energy
should be equal to the van der Waals-energy, i.e. ~8 kcal in this
case. Am I wrong with my assumptions? Could anybody clear things out
for me?
Best regards,
Samuel
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Received on Wed Feb 24 2010 - 01:30:03 PST
