[gmx-users] protein and ligand is not forming complex after completing simulation

[Swagata Patra]

For trjconv i used the following command:

trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol -ur
compact -dt 30000

For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb

I have analyzed the H-bonds between protein and ligand, there showing
formation of H-bonds.

if ligand is dissociating, what could be the reason?


On Wed, Jul 27, 2016 at 5:40 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> Hi Swagata,
>
> Perhaps your ligand is dissociating during the simulation. What frames are
> you looking at with trjconv and editconf? If these are different you may
> be seeing bound and unbound snapshots.
>
> Best wishes
> James
>
> > hi everyone,
> >
> > I  simulated protein-ligand complex for 30ns and then visualize the
> > complex
> > after simulation in pymol.
> >
> > I got the .pdb file using two commands from final simulated file.
> > One is using trjconv, from .xtc to .pdb. When I am visualizing this .pdb
> > file, protein and ligand has not formed any complex.
> > Another one is using editconf, from .gro to .pdb. When I am visualizing
> > this .pdb file, protein and ligand  formed  complex.
> >
> > Why is this happening? Can anyone explain it?
> >
> > Thanks in advance.
> >
> > --
> > Swagata Patra
> > M.Tech (Biotech)
> > JRF
> > IIT Guwahati
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send
> > a mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati