AMBER Archive (2008)

Subject: Re: AMBER: drug/protein interaction modeling setup

From: Barbault Florent (
Date: Mon Oct 20 2008 - 15:37:24 CDT


I know this typical problem for ligand/protein complex. I think the
problem arise from the antechamber prepi command which works with
internal coordinates.

The solution I found is:

- Do a prepin file (ligand.prep) with a command like:
antechamber -i ligand.pdb -fi pdb -o ligand.prep -fo prepi -c bcc -rn
parmchk -i ligand.prep -fi prepi -o ligand.frcmod

The antechamber software will give you a file called ligand.prep and
also another file called NEWPDB.PDB, where there are all correct

- With the ligand.prep file do a ligand.lib:
source leaprc.gaff
loadamberprep ligand.prep
saveoff ligand.lib

- Now, do a library file with the correct coordinates:
source leaprc.gaff
LIG = loadpdb NEWPDB.PDB
saveoff ligand_coord.lib
(of course, xleap or tleap will say that it doesn't understand atom
types but there is no problem)

Finally, in a text editor, copy the correct coordinates (x, y and z
table) from the lib file ligand_coord.lib and paste them into
ligand.lib. The coordinates in a lib file are after
"!entry.LIG.unit.positions table dbl x dbl y dbl z". Then save your
ligand.lib file.

Your library file is OK. To make a complex in xleap, you can do
something like:
source leaprc.gaff
source leaprc.ff03
loadoff ligand.lib
mods = loadamberparams ligand.frcmod
PROT = loadpdb protein_alone.pdb
COMP = combine {PROT LIG}
saveamberparm COMP complex.prmtop complex.crd
saveamberparm PROT protein.prmtop protein.crd
saveamberparm LIG ligand.prmtop ligand.crd

I hope this will help. Tell me if you have problems.

Best regards
Florent Barbault

On Mon, 20 Oct 2008 15:10:52 -0500
  "Sean Johnston" <> wrote:
> Hey all you AMBER users,
> I'm trying to get LEaP to help me out with this liganded protein
> interaction, and I can't seem to make it all work out. I extracted
> ligand from the pdb file, putting hydrogens on so I could put it
> antechamber and assign atom labels and bond/angle parameters. After
> my prepin file, I loaded everything into LEaP and proceeded to load
>in the
> protein. I first tried in tleap, but that gave me really weird
>topology and
> coordinate files, and then when I did it in xleap, I noticed that
> coordinates had changed somewhere along the line, so now the ligand
> anywhere else near the protein. Is there something in LEaP or
> that would mess with the coordinates of the ligand/protein? Thanks
>for the
> help, and I could provide a couple more specifics... I'm late for
> Oh, and is there a standard way to make this work? Am I going about
> correctly?
> -Sean Johnston
> Sean Johnston

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