[gmx-developers] Query on g_mmpbsa in gromacs

Prasanna D R bt14d031 bt14d031 at smail.iitm.ac.in
Sat Mar 26 07:19:43 CET 2016


I have been using g_mmpbsa of Rashhmi Kumari and group to calculate binding
energy of lipids in protein-lipid complex. I got a quite good results with
g_mmpbsa. Now, In my next step I need to perform network analysis where
pairwise interaction energy from mmpbsa will be considered.

I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
generated residue decomposition energy of aminoacids with lipid (not
between aminoacids) as shown below  (for example purpose)

1            1.0784
2            -0.0261
3            0.9493
4            0.0206
5            -0.0583
6            0.0061
7            -0.0278

While running mmpbsa my first input was protein and second input was lipid
(in place of ligand). Now I have interaction energy of each aminoacid with
lipid .

Now,  I need interaction energy between aminoacids. like 1st aminoacid with
remaining 499  aminoacid and 2nd with remaining 499 aminoacids and so on.

Is it possible to calculate interaction energy between amnoacids and with
lipids using g_mmpbsa (n X n matrix of energy values) ?

Please help me in this regard.
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