Protocol Sheet: ACETK.PRMAMBER.v1

Parametrizing a ligand with Amber's GAFF forcefield

Author: Toni Giorgino (acemd@googlegroups.com)
Copyrights 2011, University Pompeu Fabra. All rights reserved.
Software requirements: AmberTools.
Knowledge requirements: Basics of molecular modelling.
Input requirements: See below.

Disclaimer. This protocol is based on a best practice. In no way, we guarantee that it is optimal for your system. You use it at your own risk.

Example files

Download them here.

Basic procedure

The following sequence reads a ligand_1.pdb file, and generates ligand_1.prepi and ligand_1.frcmod, necessary to build systems with tleap or xleap including said ligand. The residue will be referenced as 'MOL'. Partial charges will be computed with the AM1-BCC/SQM method. Different methods can yield different estimates for partial charges (see below).

Step 1: Prerequisites for the input

For the following procedure to work, you will need the ligand's structure and the following:

AmberTools 1.4 should be installed and the AMBERHOME environment variable set accordingly
PDB file with coordinate information (e.g., ligand_1.pdb)
atoms should be ATOM, not HETATM, in the PDB
explicit hydrogens should be present
ligand's atom names should be unique (on all atoms, including hydrogens)
protonation states appropriate for the simulation conditions
total charge should be know (e.g., -nc 1 for +1)
only one stereoisomer

Please see the "solution to common problems" section if some of the conditions are not met.

Step 1: Generating the PREPI fragment

The Antechamber program (part of AmberTools) is invoked to generate a prepi file. A prepi file contains geometry and partial charge information on the ligand to be modelled, and is read as input by tleap. Here we use Antechamber to convert the geometry, infer GAFF atom types, and do the partial charge computation with an assumed total charge of +1 e into ligand_1.prepi.

$AMBERHOME/bin/antechamber -fi pdb -i ligand_1.pdb -fo prepi -o ligand_1.prepi -nc 1 -pf y -rn MOL -c bcc

Step 2: Generating parameters

Ligand-specific parameters not included in the GAFF forcefield should now be guessed with the following command:

$AMBERHOME/bin/parmchk -i ligand_1.prepi -f prepi  -o ligand_1.frcmod

This will generate the ligand_1.frcmod file, which we shall use at the next step. The content of the file should be inspected for poorly-guessed values.

Step 3: Check

The following commands will create a system containing the modelled ligand. If it succeeds, you may embed the ligand in more complex systems.

$AMBERHOME/bin/tleap -f leaprc.gaff 
   loadamberprep ligand_1.prepi
   loadamberparams ligand_1.frcmod
   check MOL
   saveAmberParm MOL ligand_1a.prmtop ligand_1a.crd 
   savePDB MOL ligand_1a.pdb

If successful, you will get a ligand_1a.prmtop and ligand_1a.pdb that can be used to run the simulation.

Alternate methods to compute partial charges

AM1-BCC with MOPAC

This is the method used in older versions of Antechamber.

$AMBERHOME/bin/antechamber -fi pdb -i ligand_1.pdb -fo prepi -o ligand_1.prepi -nc 1 -pf y -rn MOL -c bcc -df 0
$AMBERHOME/bin/parmchk -i ligand_1.prepi -f prepi  -o ligand_1.frcmod

RESP charges with Gaussian

This requires the Gaussian software. Electrostatic density is computed on the optimized geometry at the HF/6-31G* level of theory by default.

$AMBERHOME/bin/antechamber -fi pdb -i ligand_1.pdb -fo gcrt -o ligand_1.gcrt -nc 1 -pf y -rn MOL -c gcrt
g03 ligand_1.gcrt > ligand_1.gout
$AMBERHOME/bin/antechamber -fi gout -i ligand_1.log -fo prepi -o ligand_1.prepi -nc 1 -pf y -rn MOL -c resp
$AMBERHOME/bin/parmchk -i ligand_1.prepi -f prepi  -o ligand_1.frcmod

Solutions to common problems

Atom names in PDB are not unique. These can be made unique with the following command $AMBERHOME/bin/antechamber -fi pdb -i ligand_1.pdb -fo pdb -o ligand_1_uniq.pdb.
HETATM instead of ATOM. Fixed with the following command sed -i 's/HETATM/ATOM /g'
Multiple stereoisomers should be treated as different molecules if they cannot convert with each other during a simulation
Missing explicit hydrogen atoms, protonation states, total charge can be computed within MarvinSketch.
Molecule not in PDB format. Use MarvinSketch or openbabel to convert it.