[gmx-users] (no subject)

[zaved at tezu.ernet.in]

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


* * * D I S C L A I M E R * * *
This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message.