AMBER Archive (2009)
Subject: [AMBER] Sander
Date: Mon Apr 06 2009 - 08:17:34 CDT
Dear Amber users,
I am using Sander to calculate the 3D structure of a biopolymer. In Sander section of the AMBER10 manual there is a statement says:
" In addition, a key strength of the program is its ability to carry out the refinements (usually near the final stages) using an explicit-solvent representation that incorporates force fields and simulation protocols that are known to give pretty accurate results in many cases for unconstrained simulations; this ability should improve predictions in regions of low constraint density and should help reduce the number of places where the force field and the NMR constraints are in "competition" with one another"
I was wondering, how can I use this strength in my calculation, since I have a low constraints density part. is there any tutorial or any explanation for that ?
Thank you in advance.
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