The choice of the C3 atom type for ildn was unfortunate, since I think some
of the (old?) Amber force fields had previous plans with it. The code to
assign radii is found in 2 places: LEaP and ParmEd. The code in ParmEd is
a bit more straightforward, since it is separated out by radius set, and
LEaP converts the bondi set to an internal code which is not entirely
obvious.
The radii are assigned in leap, but beginning with AmberTools 12 they can
actually be changed via ParmEd. The problem in your case is that the ILDN
modifications changed CG2 in ILE from CT (radius 1.8) to C3 (radius 2.2).
(The Python version of the radius assignment code is in
$AMBERHOME/AmberTools/src/parmed/ParmedTools/changeradii.py).
Probably the easiest thing to do (since this radius was intended to be 1.8)
is to physically change the CG2 radius to 1.8 in the topology file. This
is very easy with ParmEd (either the GUI xparmed.py or the CLI parmed.py).
Look for the "change" command, then change the RADII of :ILE.CG2 to 1.8
(then, of course, write out a new topology file). With parmed.py, it would
look something like this:
parmed.py your.prmtop << EOF
changeRadii mbondi3
change RADII :ILE.CG2 1.8
parmout new.prmtop
EOF
The first command makes sure that you start from the mbondi3 radius set
(unnecessary if you set it in leap). The second command, "change", will
allow you to change any atomic properties (e.g., ATOM_NAME, CHARGE, MASS,
RADII, etc.), so we change the RADII property of a given mask to the
assigned value. This will change every ILE.CG2 atom in your system to 1.8.
HTH,
Jason
On Tue, Sep 11, 2012 at 9:14 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> The same problem occurs with igb=8 and mbondi3, the CG2 atom in ILE (C3
> type) is assigned a radius greater than 2 and sander exits with same
> error I reported for igb=7 and the "bondi" radii set.
> Of course checking the topology file for all assignments is rather
> tedious and I would be happy to avoid that if possible. So, probably the
> most easy solution becomes to use the original ff99SB force field for
> the implicit simulations and switch to the desired modified force field
> for the subsequent explicit solvent simulations. Not a very elegant
> solution but I guess an acceptable one for now.
>
> Can anybody tell me where under the amber source tree are these radii
> sets stored ? Are these hard coded ? I could not find any file that
> contains the radii sets ..
>
> Best
> Vlad
>
> On 09/10/2012 03:25 PM, Carlos Simmerling wrote:
> > oh yeah, I see it now. that's what I get for trying to answer questions
> > early in the AM!
> > I do not at all recommend igb=7. the underlying model is good, but the
> > parameters were not well optimized. We refit them for igb=8 and the
> > performance is far better. you'll also want mbondi3 radii.
> >
> > the easiest way for you to debug this is to actually look at the radii
> that
> > leap assigned in each of the cases. It could indeed be that the ILDN atom
> > types aren't compatible with the radii logic in leap- typically leap does
> > need to know more than just the element in order to set the radii.
> getting
> > an error is the best case- it's possible to set them incorrectly for your
> > molecule and actually get bad behavior without an error.... leap really
> > doesn't know that much about chemistry.
> >
> > On Mon, Sep 10, 2012 at 9:20 AM, Vlad Cojocaru <
> > vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> >
> >> Carlos,
> >>
> >> I mentioned already I am using AMBER 12 ... But it was kind of between
> >> the lines .. Sorry for that !
> >>
> >> Best,
> >>
> > Vlad
> >> On 09/10/2012 02:57 PM, Carlos Simmerling wrote:
> >>> how radii are set does depend on which version of Amber you have, so
> we'd
> >>> need to know that before we can help...
> >>>
> >>> On Mon, Sep 10, 2012 at 4:49 AM, Vlad Cojocaru <
> >>> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> >>>
> >>>> Dear all,
> >>>>
> >>>> It appears that the Generalized Born simulations with igb=7 or igb=8
> are
> >>>> incompatible with the ILDN modification of the ff99SB force field.
> >>>> I was trying to do an implicit solvent optimization of an unstructured
> >>>> tail before starting explicit solvent simulations, but after setting
> >>>> PBradii to "bondi" in Leap and running with igb=7 (AMBER 12), I got
> the
> >>>> error
> >>>>
> >>>> " Atom 25 has radius 2.2000000000000002 outside of
> >>>> allowed range
> >>>> of 1.0 to 2.0 angstroms for igb=7. Regenerate prmtop file with
> bondi
> >>>> radii."
> >>>>
> >>>> Looking in the topology I realized that this is a CG2 atom in ILE
> which
> >>>> has the type C3 ...
> >>>>
> >>>> If I do the same simulation with igb=5, I do not get any error .. But
> >>>> now I am actually wondering if the radii for these atom types are
> >>>> assigned properly with the set "mbondi2" (which I used for the igb=5
> >>>> simulations)...
> >>>>
> >>>> I know that ILDN modifications are optimized for explicit solvent
> >>>> simulations, but since my goal is actually explicit solvent
> simulations
> >>>> I did not want to use a different force field for the intermediate
> step
> >>>> of implicit solvent optimization.
> >>>>
> >>>> Best wishes
> >>>> Vlad
> >>>>
> >>>> --
> >>>> Dr. Vlad Cojocaru
> >>>> Max Planck Institute for Molecular Biomedicine
> >>>> Department of Cell and Developmental Biology
> >>>> Röntgenstrasse 20, 48149 Münster, Germany
> >>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >>>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>>
> >> --
> >> Dr. Vlad Cojocaru
> >> Max Planck Institute for Molecular Biomedicine
> >> Department of Cell and Developmental Biology
> >> Röntgenstrasse 20, 48149 Münster, Germany
> >> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
>
>
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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 11 2012 - 07:00:03 PDT
