AMBER Archive (2009)

Subject: [AMBER] MM-PBSA decomp by residue and snapshot?

From: Bradshaw, Richard (richard.bradshaw08_at_imperial.ac.uk)
Date: Thu Mar 05 2009 - 11:55:05 CST

Hi all,

I've been running MM-PBSA on a complex and the decomp by residue analysis has identified a few residues which contribute most to the free energy. From watching the trajectories some of these residues undergo flips/rotations at certain points in the trajectory and I'd like to know how these rotations affect the contribution to the free energy. Essentially I'd like to extract how the free energy contribution changes per residue and over the 1000 snapshots of the trajectory, so that I can plot it and possibly correlate the residue motions that I see to the big free energy changes...

So I have 2 questions:

I think the info I would need to do this is all in the .com.all.out, .rec.all.out and .lig.all.out files of the decomp analysis. I was planning to try to write a small script to extract the info I need from these files, but has anyone done this before and is aware of an easier way? Are there any adaptations to one of the mm_pbsa scripts I could use for example?

If not, does anyone know the formatting of the .com.all.out files? I've come up with something like this:

MM
GB
MS
1
TDC 1 23.281 -7.047 -30.636 -35.850 0.661

>From what I can tell, this is:

Snapshot
T/S/B Residue INT VDW ELE GB GBSUR

But obviously I'd like to check that before I carry out any calculations! Any help would be appreciated.

I've had a quick look through the manual (Amber 10) and the mailing list but couldn't find anything on this specific topic, so apologies if it's been asked before.

Many thanks in advance,
Richard 

--
Richard Bradshaw
Mres/PhD Student, Chemical Biology Centre
Tate, Leatherbarrow & Gould groups
Room 537, Chemistry C1
Imperial College London
South Kensington Campus
SW7 2AZ

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