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?
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/
Hi @simonbray, I was trying to use the ‘Create GROMACS index files’ tool in Galaxy EU but I got several warnings like WARNING:galaxy.model:Datatype class not found for extension ‘ndx’ and then the ndx file is not recognized by the ‘Create GROMACS position restraints files’ tool. Do I need to do some edit in the datatype? Many thanks!
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