AMBER Archive (2007)

Subject: AMBER: Explicit water opinion

From: Hayden Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Fri Apr 13 2007 - 13:39:19 CDT

 
Dear Amber Users

I am about to attempt an explicit water simulation on a protein (40 amino
acids) bonded to a sacharide partner. I am wondering which explicit model is
best, many papers have published findings with SPC and TIP3P boxes. However,
I've recently been to a conference in which many people derided TIP3P as
being weak. Is there any agreement as to which water representation is most
accurate? (Or at least most appropriate for a small protein with a charge of
approx. +6).

Many thanks

Hayden Eastwood

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