What Hai was saying is that "set default pbradii mbondi3" is identical to
"set default pbradii mbondi2" for all atoms except 3 atom types [HH(Arg)
and OE(Glu), OD(Asp)].
Also, the atom radii are NOT stored in the force field files (e.g.,
gaff.dat, parm99.dat, etc.). They are stored in the LEaP (and ParmEd)
source code. If you want to use the mbondi3 radii, you should load mbondi3
at the beginning -- the ligand will be treated as though the radii set was
mbondi2.
HTH,
Jason
On Wed, May 2, 2012 at 11:05 AM, Jesper Sørensen <jesorensen.ucsd.edu>wrote:
> Thank you Hai. But it is likely that the ligand radii are coming from the
> GAFF parameters.
>
> I wonder if the correct procedure would probably be to "set default
> PBradii mbondi3" before loading in the ligand - then only the protein radii
> should change to mbondi3, without trying to alter the ligand radii as well,
> which again mbondi3 was likely not parameterized for?
>
> Or will this also change the ligand radii?
>
> Best,
> Jesper
>
>
> >
> > For the ligand, mbondi3 should be exactly the same as mbondi2 since only
> > radii of HH(Arg) and OE(Glu), OD(Asp) atom type are changed in mbondi3
> from
> > mbondi2.
> >
> > Best
> > NHAI
> >
> >
> > On Apr 30, 2012, at 9:02 AM, Ray Luo, Ph.D. wrote:
> >
> >> 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 02 2012 - 13:30:04 PDT
