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 - 02:00:02 PDT
