Dear Amber user and Developer,
I've been running MMPBSA calculation but i'd like to know more about some
flag.
Since in Amber18 module there is a bit warning, it said "You should be sure
that you know how to carry out an MM-PBSA calculation “by hand” (i.e.,
without using the scripts" ( Amber 18 Manual Page 731).
My question:
1. What is the appropriate, between inp=2 or inp=1 to calculate ligan
binding ?
2. The default PBRadii is "mbondi". But in mmpbsa tutorial we said that we
should select the correct radii for the calculation method. And the
recommended setting was given in this url:
http://ambermd.org/tutorials/advanced/tutorial3/files/recommended_settings.pdf.
I'm still confused how to choose radii. Is there any recommendation for
protein-ligand binding calculation ? Some script suggest mbondi2 or
mbondi3.
3. In one of the discussion, If set entrophy=0, we wil get not true binding
energy. why ? What is the different if set entrophy=1.
Thank you for your attention
Setyanto Tri Wahyudi
-------
Biophysics Division,
Department of Physics - Bogor Agricultural University
Gedung Fisika Wing-S Lt.2 Jl. Meranti
Kampus IPB Darmaga
Bogor - 16680
Indonesia
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Received on Wed Aug 01 2018 - 05:00:03 PDT
