Hi there
I'm working with gromacs for ligand-protein interaction simulation. I have
run MD for docked complex and now there is a problem with trajectory
visualization by VMD. The ligand has left binding site circulating around
the protein.
I tried to fix the problem by making index and extract the
On 9/15/15 7:39 AM, Homa rooz wrote:
Hi there
I'm working with gromacs for ligand-protein interaction simulation. I have
run MD for docked complex and now there is a problem with trajectory
visualization by VMD. The ligand has left binding site circulating around
the protein.
I tried to fix the
Dear Justin
I have followed your advice but it didn't solve my problem.
Ligand is still out of binding site.
--
Homa Ahmadi
Shahed University
Faculty of Basic Sciences
Alternative email> h.ahm...@shahed.ac.ir
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On 9/15/15 1:24 PM, Homa rooz wrote:
Dear Justin
I have followed your advice but it didn't solve my problem.
Ligand is still out of binding site.
Can you verify that it actually did start in the binding site? Was everything
built correctly? If so, there's no reason that simply centering
Maybe the ligand actually is leaving the binding site and moving
around, and that's what your simulation is telling you! Hard to say
with the posted information.
On Tue, Sep 15, 2015 at 11:24 AM, Homa rooz wrote:
> Dear Justin
> I have followed your advice but it didn't solve my problem.
> Ligan
>6. Re: Accelerating data analysis. (Dawid das)
>7. Re: Accelerating data analysis. (Dawid das)
>
>
> --
>
> Message: 1
> Date: Tue, 15 Sep 2015 16:09:15 +0430
> From: Homa rooz
> To: gromacs.org_gmx-users@ma
On 9/16/15 1:23 AM, Homa rooz wrote:
Dear Justin
If you asked about verifying docking process. I should say, I have worked
with single chain protein and the best ranked binding energy was -7.41
kcal/mol by AutoDock 4.2, considering that binding site was located on turn
structure and the edge
