[gmx-users] Protein-Ligand Interactions

Smith, Micholas D. smithmd at ornl.gov
Fri Aug 7 13:59:58 CEST 2015


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.


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 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

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

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