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.
>
> I think leap assigned the wrong radius for this C atom. I believe that
radius of ALL C atoms in bondi, mbondi2 or mbondi3 should be 1.7 A.
> 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
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
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> >>> 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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> >
> >
>
> --
> 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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Received on Thu Sep 20 2012 - 14:30:03 PDT
