Hi Jason,
One last question. Since when has mbondi been the standard in leap? Always? Do you know?
Best,
Jesper
On May 3, 2012, at 8:56 AM, Jesper Sørensen wrote:
> Great for clearing that up.
> Thank you Jason and others who have contributed their time and knowledge to this thread.
>
> Best regards,
> Jesper
>
>
> On May 2, 2012, at 5:00 PM, Jason Swails wrote:
>
>> On Wed, May 2, 2012 at 7:21 PM, Jesper Soerensen <jesorensen.ucsd.edu>wrote:
>>
>>> Hi Jason,
>>>
>>> I know and that does make sense, since the changes only pertain to the
>>> protein. But then mbondi2 were not made for ligands either - correct?
>>> So should the ligand radii not come from the gaff parameters, or am I
>>> misunderstanding something and gaff does not contain/specify its own set of
>>> GB radii but instead use the mbondi2 radii?
>>>
>>
>> As far as I know, they were not developed with small ligands in mind.
>> However, my understanding is that GB does reasonably well for small
>> ligands, since it's not a significant perturbation from the Born solution
>> to the PB equation (from which GB is based). The complexity arises when
>> you try to treat very complex systems like proteins.
>>
>> Globular proteins are obviously significantly different than a simple
>> sphere, and so the correct estimation of the effective Born radius (which
>> more or less measures proximity to the bulk solvent) becomes essential to
>> properly characterize the solution-phase behavior. This is what the
>> intrinsic radii from %FLAG RADII are used for (and *only* this in GB
>> calculations). As a result, you should consider these radii a parameter of
>> the GB model you're using, not of the force field you're using. (So no,
>> gaff does not contain its own set of GB radii, nor does any other Amber
>> force field).
>>
>> A gaff carbon that is sp2-bonded carbon with a double-bond to an oxygen is
>> for all intents and purposes identical to the backbone C atom of an amino
>> acid with respect to relative size and is therefore treated the same with
>> the LEaP-assigned radii. Moreover, I argue this is the appropriate
>> behavior given the purpose these radii serve.
>>
>>
>>> Also, is mbondi2 the standard PB radii in leap now?
>>>
>>
>> No, 'mbondi' is (at least using ff12SB).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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Received on Thu May 03 2012 - 14:30:04 PDT
