[gmx-users] distance between protein and ligand

[Archana Sonawani]

Hi  Liu Shiyong,

No, I didn't repeat any simulation. My intention is to compare two large
compounds with our designed molecule which is comparatively smaller.

On Wed, Oct 10, 2012 at 6:01 AM, Liu Shiyong <liushiyong at gmail.com> wrote:

> Hi,
>
> 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."
>
> Best
>
> Shiyong
>
>
> 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
> Tel：86-27-87558335-805
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-- 
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339