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
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> >
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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 Sat Apr 28 2012 - 14:00:03 PDT
