I think what Niel said is correct.
Best,
Qin
On Apr 30, 2012, at 12:34 PM, Ray Luo, Ph.D. wrote:
> 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 - 13:00:03 PDT
