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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Received on Mon Sep 10 2012 - 06:00:03 PDT
