[AMBER] differences in counterion position with water models and questions

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Fri, 7 May 2021 11:37:13 +0530

Dear All,
I am seeing some differences in the position of counterions with tleap that
I think might have some impact on how conformations evolve during MD.
This protein has an FMN co-factor.
Following are the differences that I'm observing and some associated
1) with ff14sb/tip3p, Na+ ions are placed away from the dianionic FMN
phosphate group.
2) with ff19sb/opc, Na+ ions are placed close to FMN that form close
contact during equilibration. This ion doesn't move away from FMN during a
40ns MD.
3) with ff19sb/opc, K+ ions are placed far away from FMN (may be due to
large Van der Waals radii of K+).

1) Since most exp. are done in KPi buffer to mimic intracellular
conditions, why do many studies use Na+ ions for such proteins? Is it not
better to always use K+ ions and avoid using Na+ (unless there are other
reasons for using them)?
2) Can the differences in the choice of these counterions have a
significant impact on the dynamics of the protein and complexes? (I think
it may). There is some literature on ions vs. no ions (here
<https://academic.oup.com/peds/article/14/10/747/1498769>and here
<https://academic.oup.com/peds/article/14/10/747/1498769>), but I can't
find comparisons between Na+ vs K+.
3) Is it possible to selectively include/exclude a region where counterions
can be placed by tleap?
4) Is there a difference between the two commands "solvatebox mol opc 10"
and solvatebox mol *opcbox *10"? the first did not give any error and
simulations are running fine, but not sure if it is correct usage.

Looking forward to valuable suggestions and tips from the list.
thank you and best regards.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Thu May 06 2021 - 23:30:03 PDT
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