On Tue, Apr 04, 2017, Ramin Salimi wrote:
>
> I am trying to use GB/SA model to calculate the internal energy
> of my DNA molecule by stripping water molecules from the solvated
> trajectory. But I do not know the updated GB/SA methodology. And I
> checked the references in Amber16 manual and it refers to the following:
>
> Tsui, V.; Case, D. Molecular dynamics simulations of nucleic acids
> using a generalized Born solvation model. J. Am. Chem. Soc., 2000, 122,
> 2489–2498
> Tsui, V.; Case, D. Theory and applications of the generalized
> Born solvation model in macromolecular simulations. Biopolymers
> (Nucl. Acid. Sci.), 2001, 56, 275–291
The best thing to read is Chapter 4 of the 2016 Reference Manual (and you
should go ahead and download/install AmberTools16.) We recommend using igb=8
for both proteins and nucleic acids.
>
> I would really appreciate if one can give me guidance on updated GB/SA
> methodology( if there is any) and how to implement it through the
> control variables? Is the internal energy shown as EGB in each step in
> the output file?
EGB is the estimated solvation free energy, which is added to all the other
terms to get the total potential energy.
> I am using Amber14 and have checked the directory
> amber14/test/gbsa_xfin. But I am not sure if this is the input file that
> I should be applying to my system.
That is a good example input, but see the comments above about igb. Tutorial
B3 also walks you through running a GBSA simulation.
...hope this helps...dac
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Received on Tue Apr 04 2017 - 05:30:05 PDT
