AMBER Archive (2006)

Subject: Re: AMBER: mixing GAFF and CHARMM

From: Ravinder Abrol (pointfielder_at_yahoo.com)
Date: Wed Dec 20 2006 - 18:58:36 CST

Thanks Chris. Your experience is quite helpful in this regard.
We normally use quantum charges for ligands and have scripts
to generate charmm compatible toppar files from antechamber
output. I am looking into the charmmgen options now.
Ravi

----- Original Message ----
From: Christophe Guilbert <cguilbert_at_picasso.ucsf.edu>
To: amber_at_scripps.edu
Sent: Wednesday, December 20, 2006 11:51:18 AM
Subject: Re: AMBER: mixing GAFF and CHARMM

Ravi,

I am using CHARMM parameters for protein and nucleic acid mixed with
GAFF (trough Antechamber) for the ligands. I don't really have a
scientific justification for doing so, but my docking using those mixed
FF are doing just great. In general , the charge given by
GAFF/Antechamber (am1-bcc) is rather good and give similar charges than
CHARMM for the same ligand. VDW parameters are different, how different
? well they are .... you can modify GAFF VDW parameters to match those
of CHARMM if not satisfied.
They are also some problems with some Nitrogen not being trigonal planar
for some different reasons , but Junmei Wang (the father of Antechamber)
fixes those problems when they come.
but again I do some pretty accurate docking prediction using both mixed FF.

2 tips:
- Have a look to charmmgen.c and charmm.c in Antechamber package.
- you have a module in INSIGHT which is supposed to calculate the
ligand topology and parameters fully compatible with CHARMM , I never
used it . Love antechamber too much !!! ;-)

Hope this help.

Chris

Ravinder Abrol wrote:
> Hi All,
> We are looking at protein-ligand complexes embedded in lipids and I am curious to find out
> if someone has experience using GAFF parameters for ligands and CHARMM parameters
> for the rest of the system (protein and lipids). Can GAFF (being a generalized FF) be mixed with
> CHARMM in this way to carry out MD simulations? Thanks.
> Ravi
>
>
> 

-- 
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