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
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