[gmx-users] (no subject)

RAHUL SURESH drrahulsuresh at gmail.com
Wed Aug 16 08:05:14 CEST 2017

I suggest check for the appropriate binding pocket. See whether the ligand
relocates at some other point in protein or keep to stay away. Also check
for the quality of the topology generated.

On Wed, Aug 16, 2017 at 10:11 AM, <zaved at tezu.ernet.in> wrote:

> Hii Everyone
> I had performed a 100ns protein-ligand (docked complex) simulation with
> gromacs 5.1.4.
> The ligand in my case is hydrogen peroxide.
> I have removed the PBC effect and centered the protein.
> I have used the following commands:
> gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc
> gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc
> I am analyzing the average distance between the protein and the ligand. I
> am getting a value of 3.2nm which is too high.
> Also in the out_1.xtc, after 10ns itself the ligand is moving all around
> the protein.
> Unable to understand why its happening!!
> Please suggest.
> Thank You
> Regards
> Z. Hazarika
> Research Scholar
> Tezpur University
> Tezpur, India
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*

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