[gmx-users] Protein-Ligand Interactions

[su]

Thank You very much Sir 
I will do as you mentioned and will inform after viewing. 
Best Regards
Suniba

Sent from my iPhone

> On 07-Aug-2015, at 5:28 pm, "Smith, Micholas D." <smithmd at ornl.gov> wrote:
> 
> Suniba,
> 
> What exactly did you do to convert your trajectory to a .xtc? If you used trjconv -pbc mol (or other options) then you need to make sure you have selected both ligand + protein as outputs. One way to do this is to build an index with make_ndx that contains your both your protein and ligand as one group and then select it as your output in trjconv.
> 
> Example.
> 
> make_ndx -f (your grofile here) -o index_withprotein+ligand
> trjconv -f -s -pbc mol -n index_withprotein+ligand -o md_0_1_noPBC.xtc
> 
> -Micholas    
> 
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> 
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of su <sun.iba2 at gmail.com>
> Sent: Thursday, August 06, 2015 5:23 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Protein-Ligand Interactions
> 
> Hello
> I have posted this query already but in absence of any suggestion,i am posting it again. After completion of protein-ligand MD, I tried to visualize the trajectory in VMD.It shows only protein and my ligand is absent. To view hydrogen bond interactions between pro-lig, i have gmx hbond, that showed the number of donors and acceptirs but again visualising problen. Can anyone help me to know how to view the protein and ligand together and the interactions between them. Or is it this way only that in md.gro file and the md_0_1_noPBC.xtc, no ligand is present?
> Best regards
> Suniba
> 
> Sent from my iPhone
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