[Dock-fans] Amber RESP charges in DOCK

Scott Brozell sbrozell at scripps.edu
Wed Apr 9 17:41:36 PDT 2008


Hi,

On Tue, 8 Apr 2008, snoze pa wrote:

>  I am wondering if I can use the RESP charges (defined in AMBER
> forcefield) in preparing the DOCK6 mol2 file.
> I know the resp chearges are not exatly the charges calculated using
> MOPAC or other software toold. Any suggestion?

One can use any charges.

Getting the charges into the DOCK ligand mol2 input file will
need to be done manually.  Chimera's dock prep does not support
RESP; this link is still apt:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/001963.html

Amber offers tools for helping with the quantum.
I would probably use antechamber after I had the quantum chem
calcs completed:

antechamber -s 2 -i ligand.gout -fi gout -o ligandresp.mol2 -fo mol2 -c resp


The DOCK Amber score preparation scripts do not support non-AM1BCC
charge models.  This feature will exist in 6.3.

Scott




More information about the Dock-fans mailing list