[gmx-users] questions related to MD of protein-ligand complex

[Brett]

Dear All,


There is the on-line Justin Protein-ligand MD tutorial, but my protein complex contains 4 identical subunits and each subunit contains a ligand. In this situation should I prepare 4 ligand files using the ligand file preparation tools external to GROMCS? And what extra attention I should take for preparing the complex.gro and topol.top for this 4-ligand complex?


For the "topol.top", the on-line tutorial has a sentence " Just insert a line that says #include "drg.itp" into topol.top after the position restraint file is included". Here what does it mean for the "position restraint file", and where has been included in the on-line tutorial (example files)?


Brett