In particular if you could point me to where I might obtain the GBneck2
parameter file, that would be be really helpful.
On Sun, Jan 28, 2018 at 2:22 PM, Siddhartha Jain <tmfs10.gmail.com> wrote:
> I wanted to know where the files that have the parameter sets are as I
> need to compute the Hessian of the MM-GBSA energy function. But it seems
> there might be a way to get the Hessian via the mme2 function in NAB? I'm
> not sure how to go about it however so if you have pointers on how to call
> that function in python, that would be really good.
>
> Thanks!
> --Sid
>
> On Sun, Jan 28, 2018 at 9:59 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> Can you be more specific about what you mean by GBSA parameters? Amber has
>> several GB parameter sets, with the most recent being the igb=8 model
>> ("GBneck2"). You can read more about it's development here:
>> Improved Generalized Born Solvent Model Parameters for Protein Simulations
>> Nguyen, H., Roe, D. R., Simmerling, C., Journal of Chemical Theory and
>> Computation, 2013, 9 (4), 2020-2034
>> DOI: 10.1021/ct3010485
>> PMCID: PMC4361090
>>
>> and testing with ff14SB here:
>> Folding Simulations for Proteins with Diverse Topologies Are Accessible in
>> Days with a Physics-Based Force Field and Implicit Solvent
>> Nguyen, H., Maier, J., Huang, H., Perrone, V., Simmerling, C., Journal of
>> the American Chemical Society, 2014, 136 (40), 13959-13962
>> DOI: 10.1021/ja503277669
>> PMCID: PMC4195377
>>
>> ff14SB does not have a dielectric constant, that would be a property of a
>> specific material that you simulate rather than the force field itself.
>>
>>
>> On Sat, Jan 27, 2018 at 8:11 PM, Siddhartha Jain <tmfs10.gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > Where can I obtain the GBSA parameters for the different atom types (I'm
>> > using the ff14SB force field but fine with using others if there isn't a
>> > set of GBSA parameters for the atom types in that FF).
>> >
>> > Also what's the dielectric constant for ff14SB?
>> >
>> > Thanks
>> > --Sid
>> >
>> > --
>> > https://tmfs10.github.io
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>>
>
>
>
> --
> https://tmfs10.github.io
>
--
https://tmfs10.github.io
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Received on Sun Jan 28 2018 - 13:30:01 PST
