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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 10 2012 - 06:30:03 PDT
