[AMBER] how is pH treated in Amber - other than constant pH simulations

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Fri, 16 Apr 2010 19:44:36 +0400

Dear Amber users,
when I am looking for questions about pH and Amber I get mostly information about constant pH simulations. But what pH is supposed to be by default, without constant pH simulations? Just neutral or what it depends from?
As I understand in Amber pH is mostly set by protonation state of the molecules, so if not going to constant pH simulation I can approximately imitate some pH by setting corresponding protonation state distribution of amino acids. If physiological pH is required for protein simulation what can be general recommendation here - instant pH or default pH treatment?

Sincerely yours,

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Received on Fri Apr 16 2010 - 09:00:04 PDT
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