On Fri, Mar 3, 2017 at 4:01 AM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear Amber users,
>
> I did mm-gbsa calculation for my protein-ligand complex.
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> ------------------------------------------------------------
> -------------------
> BOND 0.0000 0.0001
> 0.0000
> ANGLE -0.0000 0.0000
> 0.0000
> DIHED -0.0000 0.0001
> 0.0000
> VDWAALS -38.3805 3.4143
> 0.2408
> EEL -17.4658 6.7954
> 0.4793
> 1-4 VDW -2091.2911 525.5238
> 37.0676
> 1-4 EEL 25.3459 0.6995
> 0.0493
> EGB 39.2494 7.4730
> 0.5271
> ESURF -5.2113 0.4671
> 0.0329
>
> DELTA G gas -2121.7915 525.8067
> 37.0875
> DELTA G solv 34.0381 7.2074
> 0.5084
>
> DELTA TOTAL -2087.7534 525.4087
> 37.0595
>
>
> Are 1-4 VDW and 1-4 EEL Energy Components important?
>
Yes. All terms are important.
What is the definition of them?
>
It is the Lennard-Jones and electrostatic interactions between atoms that
are separated by 3 bonds (i.e., that form a dihedral angle). These are
handled "separately" because they are scaled by 1/2 and 1/1.2, respectively.
For a single-trajectory MM/PBSA binding calculation, these values have to
be zero, since they should cancel exactly (like the bond, angle, and
dihedral terms). It looks to me like they do *not* cancel, but the other
bond terms do. This is a certain indication that something has gone wrong
(and you should have seen a warning about it at the top of the output file).
HTH,
Jason
--
Jason M. Swails
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Received on Fri Mar 03 2017 - 06:30:02 PST
