Re: [AMBER] Questions about TI calculation

From: <>
Date: Thu, 5 Sep 2013 03:16:51 -0400 (EDT)


> 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?

In principle you are right, if you only change vdW terms, only those can
contribute to DVDL. But in the tutorial, I believe you are really

a) a chargeless hydrogen into a chargeless OH group

and simultaneously

b) all remaining non-zero partial charges of the ligand, so it is not
completely chargeless

Your crgmask will probably be something like :LIG.H6, not just :LIG

So effectively two transformations take place together, H->OH with
softcore and charges(BNZ)->charges(PHE) with linear scaling. This can be
confusing since your ligands are neutral overall, but have non-zero
partial charges. On top of that, the ligands with crgmask set for one
functional group will not even be neutral in this step.

I hope this explains your question. Another thing to take from this is
that the breakdown of energies from this step can not be interpreted in a
meaningful way, only once you combine all three steps is the result
physically relevant.

Kind regards,

Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Sep 05 2013 - 00:30:03 PDT
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