[gmx-users] distance between protein and ligand

Liu Shiyong liushiyong at gmail.com
Wed Oct 10 02:31:39 CEST 2012


Did u repeat your MD simulation of your docked complex ?

I also asked the similar question. Alex replied :" I would start
several (5-10?) runs with different (random) starting impulse to get
more reliable data."



On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani <ask.archana at gmail.com> wrote:
> Hi,
> I have simulated a protein-ligand complex for 5ns. I checked distance
> between the important residues of protein and the ligand using g_dist. My
> question is can the distance between the two groups decrease  from the
> initial distance (docked complex as starting structure for simulation). I
> know it may increase or may remain same at the end of the simulation.
> for example: starting distance is 0.77nm and final distance is 0.8nm but
> the intermediate course of simulation (around 3ns) it has decreased upto
> 0.65. The complex shows stability after 2ns. While the SASA between the two
> groups is around 6.3 nm2  throughout the simulation which is very high.
> This is very contradicting result. Is something wrong in the simulation?
> Thanks in advance.
> --
> Archana Sonawani-Jagtap
> Junior Research Fellow,
> Biomedical Informatics Centre,
> NIRRH (ICMR), Parel
> Mumbai, India.
> 9960791339
> --
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Shiyong Liu
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Chinese Version:
华中科技大学物理学院  生物物理模建小组

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