Re: [AMBER] mbondi3

From: Ray Luo, Ph.D. <>
Date: Mon, 30 Apr 2012 09:02:53 -0700


Just a comment on a specific point in your email ...

If you set radiopt=1 and have ligand (GAFF atoms) in the system, PBSA
would drop a bomb and quit. I believe this is the designed behavior.
This is because we don't have a "rule" to define the generic atomic
types in organic molecules. As you can image, the rule would require
far more simulation data to summarize than that for the proteins/NAs.

So I don't think the scenario in your email would occur.

If you have ligand (GAFFs), the only radii you can use with PBSA right
now is those in the prmtop file and those can be read in by "radiopt =

It's not easy to mix different radii set for proteins/NAs and ligand
unless you can somehow revise the radii section in the prmtop file.


On Mon, Apr 30, 2012 at 12:11 AM, Jesper Sørensen <> wrote:
> I know (Ambertools 12, section 8.2.3) that PBSA if you use (radiopt=1), will stick to the Antechamber/GAFF radii for the ligand (and perhaps even the FF radii for the protein) if there are GAFF parameters present in the prmtop file, instead of swithing to the Tan & Luo radii (TYL06 radii). But perhaps this is only a requirement for the TYL06 radii and not mbondi* radii? Can you clarify this a bit for me?
> Best,
> Jesper

AMBER mailing list
Received on Mon Apr 30 2012 - 09:30:02 PDT
Custom Search