Dear Colleagues,
I see I should quote the last sentence of our abstract of Bradbrook et al 1998:-
This work demonstrates the difficulty in relating structure to
thermodynamics, but suggests that dynamic models are needed to provide
a more complete picture of ligand - receptor interactions.
Be
This is all true. And I think the bottom line is that it is extremely
non-trivial to get a meaningful number.
The Amber MM-PBSA script is the best established one. We have an
equivalent CHARMM-based script at:
http://www.cse.scitech.ac.uk/cbg/software/charmm/
But I guess this is beyond the origin
Dear Rex,
It certainly matters what you mean by the "energy" of a
protein ligand complex. And whether you are comparing a series
of related similar structures or looking for an "absolute"
energy.
The problem is that there is no such thing as an "absolute"
energy, it is always relative to some
Would APBS do what you want?
http://www.poissonboltzmann.org/apbs/
It has interfaces with Pymol, VMD and others...
From: Rex Palmer
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wed, October 13, 2010 6:43:49 AM
Subject: [ccp4bb] protein ligand energy
Can anyone
Dear Rex,
Not withstanding Fred's reply just to also mention that in our study:-
G.M. Bradbrook, T. Gleichmann, S.J. Harrop, J. Habash, J. Raftery,
A.J. Kalb (Gilboa), J. Yariv, I H Hillier and J.R. Helliwell “X–ray
and molecular dynamics studies of concanavalin A glucoside and
mannoside complexes:
Rex Palmer wrote:
Can anyone reccomend a free download program that will calculate the
energy of a protein/ligand complex? The ligand has been modelled in.
Thanks
Rex Palmer
Birkeck College
Hi Rex,
I think any refinement program such as CNS will do this - problem is,
since these programs
Can anyone reccomend a free download program that will calculate the energy of
a protein/ligand complex? The ligand has been modelled in.
Thanks
Rex Palmer
Birkeck College
