Hi Jacopo,
That result is probably right. The decomposition gives you the
contribution from each residue and the ligand to the total binding
energy. The contribution from the ligand will be half of the total
binding energy, the other half will come from the receptor. When you do
the decomposition you obtain the contribution from each residue towards
the total energy provided by the receptor.
So as far as I can see your result is fine.
Hope this helps,
Regards,
Bruno
On 02/02/17 17:44, Jacopo Sgrignani wrote:
> Dear colleagues
> I'm trying to calculate the contribution of single amino acid to
> the total binding free energy.
> I'm using this input file:
>
>
> Per-residue GB and PB decomposition
>
> &general
>
> endframe=500, ligand_mask=":497", verbose=1, interval=100,
>
> /
>
> &gb
>
> igb=5, saltcon=0.100,
>
> /
>
> &decomp
>
> idecomp=1, print_res="1-497"
>
> dec_verbose=1,
>
> /
>
>
> However the generated file is strange because the main contribution is
> given by the ligand.... Thus I deduced that I'm not probably
>
> calculating an interaction energy decomposition but something else.
>
> Can you help me?
>
>
> Thanks a lot
>
>
> Jacopo
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Received on Fri Feb 03 2017 - 06:30:03 PST
