Qin,
Can you comment on this?
All the best,
Ray
---------- Forwarded message ----------
From: Niel Henriksen <niel.henriksen.utah.edu>
Date: Mon, Apr 30, 2012 at 9:21 AM
Subject: Re: [AMBER] mbondi3
To: AMBER Mailing List <amber.ambermd.org>
> 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.
Actually, I think the behavior is that if GAFF atom types are present
(lowercase),
then radii from the prmtop are used. Maybe it should be changed but in
amber12/AmberTools/src/pbsa/sa_driver.F90 it says:
! for Antechamber ligands with atom types of lower cases
! use radii from the parm file
do iatm = 1, natom
if ( isymbl(iatm)(1:1) == 'h' .or. &
isymbl(iatm)(1:1) == 'c' .or. &
isymbl(iatm)(1:1) == 'n' .or. &
isymbl(iatm)(1:1) == 'o' .or. &
isymbl(iatm)(1:1) == 'p' .or. &
isymbl(iatm)(1:1) == 'f' .or. &
isymbl(iatm)(1:1) == 'b' .or. &
isymbl(iatm)(1:1) == 'i' .or. &
isymbl(iatm)(1:1) == 's' ) radi(iatm) = rin(iatm)
end do
--Niel
________________________________________
From: Ray Luo, Ph.D. [ray.luo.uci.edu]
Sent: Monday, April 30, 2012 10:02 AM
To: AMBER Mailing List
Cc: Qin Cai
Subject: Re: [AMBER] mbondi3
Jesper,
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 =
0".
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.
Ray
On Mon, Apr 30, 2012 at 12:11 AM, Jesper Sørensen <jesorensen.ucsd.edu> 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
>
>
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Received on Mon Apr 30 2012 - 11:00:03 PDT
