It depends on what systems you are using. What are the molecules in your gb
calculation?
Also even though we developed igb=8, in my opinion pbsa is a far superior
choice over gbsa unless speed is a major limitation (such as md). For
post-processing there is usually no compelling reason to choose the less
accurate gb model.
On Mon, Dec 23, 2019, 1:13 PM Rui Chen <rchen6.ualberta.ca> wrote:
> Hello,
>
> I am trying to run MMGBSA, the default parameter igb in the following
> tutorial:
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm is
> "igb = 2". However, in the AMBER manual, it mentions "The combination of
> the ff14SBonlysc force field with igb=8 gives the best results for proteins
> [20][145], nucleic acids and protein-nucleic acid complexes. [146]" I am
> using leaprc.protein.ff14SB force field, does it mean, it's better to use
> igb = 8? What's the exact difference between different igbs?
>
> If I want to run MMPBSA alone, do I only need to specify the
> "istrng" (Ionic strength in Molarity) without any GB parameters?
>
> Looking forward to your reply.
>
> Best regards,
> Rui
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Received on Mon Dec 23 2019 - 11:00:02 PST
