On Sat, Apr 5, 2014 at 12:05 AM, MOHD HOMAIDUR RAHMAN
<rahmanhpu.gmail.com>wrote:
> Dear Amber User
>
> I want to calculate " Average Interaction Energy " between residues in a
> simulation box. For this I pack x molecules of A, y molecules of B and z
> molecules of C in a box. After running MD for few ns now I have crd file.
>
> Now from crd I want to calculate the average interaction energy between
> residue A-A, B-B, C-C, A-B, A-C and B-C.
>
> I read about MMPBSA from Amber Tools 12 manual and found that they discuss
> about receptor and ligand only (only two system). While in my case the
> system is different more than two and with in residue also.
>
> Can any one please suggest me to how I will proceed to reach my goal. If
> any other way to proceed this also welcome.
>
> Thank you in advance
>
Check out the "pairwise" command in cpptraj. It is described in the
AmberTools 13 manual (p. 253). The usage is:
> help pairwise
[<name>] [<mask>] [out <filename>] [cuteelec <cute>] [cutevdw <cutv>]
[ref <reffilename> | refindex <ref#>] [cutout <cutmol2name>]
Calculate pairwise (non-bonded) energy for atoms in <mask>.
It computes the interaction between all atoms in <mask>. You can do
something like this:
pairwise aa :A out pairwise.dat cuteelec 12.0 cutevdw 12.0
pairwise bb :B out pairwise.dat cuteelec 12.0 cutevdw 12.0
pairwise cc :C out pairwise.dat cuteelec 12.0 cutevdw 12.0
pairwise ab :A,B out pairwise.dat cuteelec 12.0 cutevdw 12.0
pairwise ac :A,C out pairwise.dat cuteelec 12.0 cutevdw 12.0
pairwise bc :B,C out pairwise.dat cuteelec 12.0 cutevdw 12.0
You'll need to process the ab, ac, and bc datasets because they will
include the homogenous (e.g., A-A, B-B, C-C) as well as the desired
heterogeneous (e.g., A-B, B-C, A-C) interactions. So you will need to
subtract out all relevant homogenous interactions (which are calculated in
the first 3 lines) from the interactions you are computing.
To get the "average" interaction, you will also need to count up how many
of each species there are and divide by the total number of interactions
that are occurring based on the simple counting rules.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 06 2014 - 07:00:02 PDT
