Re: AMBER: drug/protein interaction modeling setup

From: Alessandro Nascimento <>
Date: Mon, 20 Oct 2008 18:21:05 -0200

Here is how I usually handle with this (hope it will help you):

in tleap:

source leaprc.gaff
source leaprc.ff99SB

loadamberprep ligand.prepin
loadamberaparams ligand.frcmod

complex = loadpdb complex.pdb

check complex

solvate complex ...

addions complex ....

saveamberparm complex ...

where complex.pdb is a pdb file with the ligand and the protein in the
coordinates system I want to use in the simulations. The ligand must
have all the hydrogen atoms (not really sure if it is necessary) and
the atom names should be exactly the same as used in antechamber
(necessary). Doing like this I usually avoid the ligand and protein
to be in different coordinate systems.



On Mon, Oct 20, 2008 at 6:10 PM, 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 the
> ligand from the pdb file, putting hydrogens on so I could put it into
> antechamber and assign atom labels and bond/angle parameters. After getting
> 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 the
> coordinates had changed somewhere along the line, so now the ligand wasn't
> anywhere else near the protein. Is there something in LEaP or antechamber
> 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 band!
> Oh, and is there a standard way to make this work? Am I going about it
> correctly?
> -Sean Johnston
> Sean Johnston

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Received on Wed Oct 22 2008 - 05:08:20 PDT
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