Dear Carlos,
Thank you for your reply. I am calculating MM-GBSA of a protein/small
molecule inhibitor complex. I will do MM-PBSA also. Could you please send
me script files for both MM-PBSA and MM-GBSA?
Best regards,
Rui
On Mon, Dec 23, 2019 at 11:43 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> >
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Received on Mon Dec 23 2019 - 11:00:02 PST
