Re: [AMBER] ligand topology genaration

From: Jason Swails <>
Date: Thu, 7 Jan 2016 08:21:35 -0500

On Thu, Jan 7, 2016 at 7:26 AM, neha chaudhary <>

> Hi,
> For ligand, i first used antechamber as
> >antechamber -i ligand.mol2 -fi mol2 -o ligand.prep -fo prepi
> >parmchk -i ligand.prep -f prepi -o ligand.frcmod
> >tleap
> >source leaprc.gaff
> >loadAmberParams ligand.frcmod
> >LIG = loadMol2 ligand.mol2

​This looks wrong. Your antechamber command used ligand.mol2 as an *input*
and generated ligand.prep as an output. The antechamber output --
ligand.prep -- is the file that contains the atom types and charges for
your ligand (as assigned by antechamber). Generally when people use
antechamber, they have a PDB file of their ligand and they use that to make
a mol2 file with atom types and charges. You should double-check where you
got your ligand.mol2 file and make sure you are not doing the antechamber
step twice, for instance.

Regardless of what you do​, it is the *output* of the antechamber step that
you should be loading into tleap, not the input. So this should be
something like "loadAmberPrep ligand.prep" instead of loading the mol2
file. Also, I believe that the residue name for your ligand is set inside
the prep file, so make sure that it is called "LIG" inside the prep file if
the ligand has that residue name in your complex/protein PDB file.

>saveAmberParm LIG ligand.crd
> ligand topology files generated without error.
> For protein:
> >tleap
> >source leaprc.gaff
> >receptor = loadPDB protein.pdb

​In addition to what Dave said, you *also* need to load the ligand residue
template and parameter files.​ So you need something like

loadAmberParams ligand.frcmod
loadAmberPrep ligand.prep

I highly recommend going over some of the antechamber tutorials at They will probably help clear up many


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 07 2016 - 05:30:05 PST
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