[gmx-users] Protein-Ligand

su sun.iba2 at gmail.com
Mon Aug 3 19:29:39 CEST 2015

I am confused about my MD results.According to Justin's tutorial of protein-ligand MD, i performed short 1ns md on my protein-ligand system. After completion, when i opened up the md.gro and md.xtc in VMD, it is only showing up protein.Ligand is absent from box. When i tried to view hydrogen bond interactions, it gave fatal error that no topol.trr is found. I have also prepared movie.pdb and viewed it in pymol, but in that also ligand is not showing. Can anyone please tell me if this is a common error? do i need to insert the ligand file manually? or shall i provide PBC. I can attach the files if required.

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