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.
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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>> --
>> 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 Tue Sep 11 2012 - 06:30:05 PDT
