[gmx-users] energy minimization of protein taken from PDB

[Mark Abraham]

Hi,

That value may indicate that the ligand is not horribly out of place,
because the total energy is negative. Showing a favourable binding
interaction is a different matter, for which this is just the tiniest first
step.

Mark

On Tue, Nov 11, 2014 at 9:04 AM, md kashif <kashifzamir180.mk at gmail.com>
wrote:

> Dear Dr. Justin Lemkul
> Thanks for your kind suggestion,  I have energy minimized my protein taken
> from PDB. It gives result as  -1.5248922e+06. Taking the energy minimized
> protein generated in .gro file file and docking it with ligand and doining
> energy minimization again, it gives result  as  -1.0504211e+06.
> Is this value correct? Is my ligand showing interaction and bound to my
> protein.  Please help.
>
>
> Thanking You
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