[gmx-users] Query on g_mmpbsa in gromacs

[Mark Abraham]

Hi,

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.

Mark

On Mon, 28 Mar 2016 14:37 Prasanna Dr <adveirprasanna at gmail.com> wrote:

> Hi
>
> 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
> .
> .
> .
> 450
>
> 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
> Chennai
> Tamilnadu-600036
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