AMBER Archive (2009)

Subject: Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein?

From: case (
Date: Fri Sep 11 2009 - 14:54:39 CDT

On Fri, Sep 11, 2009, cc cc wrote:
> > loadMol2 ligand.mol2 (where ligand.mol2 is created by antechamber) OR
> > loadAmberPrep ligand.prepi (where ligand.prepi is created by antechamber)
> I think both these lines MUST be included, hence it is not "OR" but
> "AND". When I tried without the prepi line but only the mol2 line, it
> did not work.

No, "OR" is correct. We very rarely create prepi files, and UCSF DOCK (for
example) uses mol2 files for creating complex prmtop files in the way outlined
above. My guess is that your failure has some other origin.


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