Hello,
I have 3 questions related to GB simulations in Amber14.
1)
In Amber14 manual there are these 2 sentences.
page 31
Currently, it appears that igb=8 may work best with the fully quantum
mechanics-based dihedral parameters included in ff14SBonlysc. Simulations
performed in explicit water most likely benefit from the empirical
corrections included in ff14SB.
page 58
The combination of the ff14SB force field with igb=8 gives the best
results for proteins;
-----
So clear is that igb=8 is actually perhaps the best choice regarding GB
algorithm for simulations of proteins but it is not so clear if in
combination with ff14SBonlysc or in combination with ff14SB.
Is it today possible to say something more clear/unambiguous about the
differences in protein simul. results between [igb=8 + ff14SBonlysc]
and [igb=8 + ff14SB] ?
2)
On page 59 there is written:
ff14SB and igb=1 is recommended for nucleic acids (see[131]for an
evaluation of GB models for DNA).
-----
Naturally one may think about the GB simulations of the mixed
protein/DNA,RNA systems.
Which igb value is recommended in that case ?
3)
Is it in Amber GB models and especially in mentioned igb=1 and igb=8
somehow explicitly treated the
hydrophobic interaction so important e.g. for bigger globular proteins ?
For the illustration, here is one recent article.
http://www.ncbi.nlm.nih.gov/pubmed/23479281
Thanks in advance for your comments.
Best wishes,
Marek
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Received on Fri Nov 21 2014 - 18:30:02 PST
