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 Mon, Apr 30, 2012 at 3:11 AM, Jesper Sørensen <jesorensen.ucsd.edu>wrote:
> Hi Jason and others,
>
> If you do specify:
>
> > "set default pbradii mbondi3" in tleap
>
> Similar to this example from the manual (Ambertools 12, section 10.2.1)
>
> > A sample script file called, for instance, mmpbsa_leap.in, is shown
> below
> >
> > source leaprc.ff99SB
> > loadAmberParams LIG.frcmod
> > LIG = loadMol2 LIG.mol2
> > receptor = loadPDB receptor.pdb
> > complex = combine {receptor LIG}
> > set default PBRadii mbondi2
> >
> > saveAmberParm LIG lig.top lig.crd
> >
> > saveAmberParm receptor rec.top rec.crd
> >
> > saveAmberParm complex com.top com.crd
> >
> > solvateOct complex TIP3PBOX 15.0
> > saveAmberParm complex com_solvated.top com_solvated.crd
> > quit
>
>
> Don't you also alter the ligand radii? Were the mbondi* radii's developed
> for this or should you stick with the GAFF parameters for the ligand?
> Again, this may just be a matter of "taste", but I figure it can't hurt
> asking.
> 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
>
>
> On Apr 28, 2012, at 1:32 PM, Jason Swails wrote:
>
> > There are two ways of specifying the mbondi3 radii in AmberTools 12. You
> > can use "set default pbradii mbondi3" in tleap (as NHAI suggested), or
> you
> > can use ParmEd (parmed.py or xparmed.py) if you already have a topology
> > file and just change the radii to mbondi3.
> >
> > HTH,
> > Jason
> >
> > On Sat, Apr 28, 2012 at 2:07 PM, Mike NG <nhai.qn.gmail.com> wrote:
> >
> >> You can specify 'mbondi3' in tleap of amber12.
> >>
> >> Best
> >> NHAI
> >>
> >> On Tue, Sep 6, 2011 at 1:56 PM, Peter Varnai <P.Varnai.sussex.ac.uk>
> >> wrote:
> >>
> >>> Dear All,
> >>>
> >>> This is to inquire whether there has been any update regarding the
> >> mbondi3
> >>> parameters for protein simulations with igb=8.
> >>>
> >>> The amber11 manual states (p. 57) that the mbondi2 radii are fine to
> use
> >>> with igb=8 which Carlos mentioned is the case indeed on 27 April but
> some
> >>> new modifications are available to improve those results for salt
> >> bridges.
> >>> The manual also details new scaling and atom-specific parameters which
> >> all
> >>> seems to have been implemented in mdread.f (apparently these can be
> >> changed
> >>> in the mdin file).
> >>>
> >>> I would be happy to update the protein atom radii in the prmtop file to
> >>> the most recent mbondi3 values: (i) has the paper been published that
> >> gives
> >>> those values? (ii) Jason's python script may be made available that
> >>> corrects for those? (iii) is there a leap fix available?
> >>>
> >>> Many thanks,
> >>> Peter
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue May 01 2012 - 22:00:03 PDT
