[gmx-users] Saving PDB with Ligand from Docking

[Mark Abraham]

Nancy wrote:
> Hello,
> 
> 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.

Mark