[AMBER] MMGB/PBSA parameters

From: Rui Chen <rchen6.ualberta.ca>
Date: Mon, 23 Dec 2019 10:12:44 -0700


I am trying to run MMGBSA, the default parameter igb in the following
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,
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Received on Mon Dec 23 2019 - 09:30:02 PST
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