[gmx-users] Query on g_mmpbsa in gromacs
mark.j.abraham at gmail.com
Mon Mar 28 17:41:21 CEST 2016
Probably you can find a way to compute a number with this non-GROMACS tool.
But is there any evidence to support that such a number will mean anything?
MM force fields are pairwise additive, not decomposable.
On Mon, 28 Mar 2016 14:37 Prasanna Dr <adveirprasanna at gmail.com> wrote:
> 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) ?
> D R Prasanna
> Research Scholar
> Computational Biophysics Group
> Department of Biotechnology
> Indian Institute of Technology Madras
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