[gmx-users] Saving PDB with Ligand from Docking
Mark.Abraham at anu.edu.au
Fri Oct 16 02:08:27 CEST 2009
> I ran a docking simulation, and I have results in .mol format, and a
> protein (.pdb format). I would like to save both as a single PDB file,
> as input for Gromacs. Please advise as to what is the best way to do this.
Sounds like the sort of thing a *docking* program should be doing for you.
With GROMACS, there's no better solution than pasting them together by
hand in a text editor, perhaps after judicious use of editconf to
translate/rotate them. You will need to take great care not to break the
format of the coordinate file.
More information about the gromacs.org_gmx-users