Dear Vlad
igb=8 should be independent to the forcefield if people don't change the
first letter for the atom name (say you should not change CA to something
like Nx). The problem is that igb=7,8 only accept radii in range of 1.0 to
2.0A. Mongan et al. developed igb7 and for some unknown reasons, he
specified this range for neck integral calculation. You can specify
'mbondi3' for igb8 or 'bondi', 'mbondi2' for igb7. If you got problem using
'bondi' radii for C atom, you should double-check if tleap assigns correct
radii.
Hai Nguyen
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 Thu Sep 20 2012 - 14:30:02 PDT
