[gmx-users] Saving PDB with Ligand from Docking

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 16 02:08:27 CEST 2009

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.


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