[AMBER] on the choosing of the cut-off value for PME with Amber14SB

From: James Starlight <jmsstarlight.gmail.com>
Date: Wed, 3 Jul 2019 15:16:52 +0200

Dear Amber users!

Normallly, using PME electrostatic cutoff around 10 angstr with
Amber99sb, I have found it as a default option with Amber99sb force
field. However, I have seen also that people se smaller cut-offs
(around 9) with amber14sb force field, which probably increase
performance of the calculations.
What the values of "cut" should be used assuming that I am dealing
with the modeling of the water soluble protein having stable
Jelly-roll domain joinded be several long loops. In terms of the
structure, these flexible segments are enriched with polar/charged
residues, which may be of the functional importance for the stability/
activity of the protein?

Thank you in advance!


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Received on Wed Jul 03 2019 - 06:30:04 PDT
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