I’m working on generating an MD simulation using Gromacs. I followed the tutorial on Galaxy training and I wanted to use Modify/convert GROMACS trajectories using trjconv tool but It requires an NDX file, I can’t find it as an output of the tools used in the tutorial. Can anyone please tell me how to overcome this problem?
@simonbray can you help me please?
Hi @Marwa, try creating the ndx file with this tool: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/chemteam/gmx_makendx/gmx_makendx/