AMBER: antechamber

From: Xin Hu <>
Date: Thu, 15 Jul 2004 14:03:44 -0400

> 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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Jul 15 2004 - 19:53:00 PDT
Custom Search