On Tue, Sep 6, 2011 at 2:38 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> the manuscript on these is under review. I think Jason's script is ready.
> mbondi2 radii are ok but mbondi3 are optimized and do indeed give much
> improved salt bridge strength and other properties.
>
I had fixed the issues my script had previously (which prevented me from
including it in the AmberTools 1.5 release). The script was a
quick-and-dirty solution to changing radii sets and is *only* capable of
setting intrinsic radii to one of the leap-specific sets (bondi, mbondi,
mbondi2, amber6) and mbondi3 (as described in the paper Carlos is
referencing), and I've attached it here.
Quite awhile ago I actually incorporated the functionality found in this
program (along with all of my other little topology file editing scripts)
into a single parameter file editor that is vastly more flexible than the
script I included here which should make many tasks easier (and a couple
others possible in the first place). This will be included (I think/hope)
with the next AmberTools release, so I'm just tossing in a little advance
advertisement here :).
To run the script I attached here, you'll need to have AmberTools 1.5
installed. This script depends on the chemistry python package directory
found in $AMBERHOME/AmberTools/src/etc/chemistry. As a result, it's easiest
if you allow AmberTools 1.5 to build its own version of python. If you do
this, then you can execute the script included as follows:
$AMBERHOME/bin/python ChangeParmRadii.py --help
That should tell you how to use it.
Hope this helps,
Jason
> 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 Tue Sep 06 2011 - 23:00:04 PDT
