AMBER Archive (2004)

Subject: AMBER: antechamber

From: Xin Hu (
Date: Thu Jul 15 2004 - 13:03:44 CDT

> Using "saveamberparm M M.crd" leap (1st run), it is going to tell
> which FF params are missing. Then, you can create your personnal FRCMOD
> (using GAFF or by fitting ab-initio data) which contains 'your' NEW FF
> that can be load into leap (in a 2nd run) i.e. using:
> xleap -f leaprc.ff99
> M = loadmol2 Mol_o.mol2
> FRCMOD = loadamberparam frcmod.Anshul
> saveamberparm M M.crd

My question is how to use antechamber to prepare input files of a
protein/ligand complex for Leap in general. As I understand, I should
extract the ligand of small molecule from the PDB (saved as Ligand.pdb), add
Hydrogens using such as Sybyl, and then derive coordination and parameter
files for the ligand:

>antechamber -i Ligand.pdb -fi pdb -o Ligand.prep -fo prepi -c bcc
>parmchk -i Ligand.prep -f prepi -o Ligand.parm

In xleap:
>source leaprc.ff99
>source leaprc.gaff
>loadamberprep Ligand.prep
>loadamberparams Ligand.parm

and then load the protein/ligand complex, save the paramter files for MD

>M=loadpdb protein.ligand.pdb
>saveamberparm M M.crd

Is there a better way to do that?
Thank you for your suggestion.


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