[AMBER] How to calculate the solvation free energy using Amber?

From: JinpengYang <1507110130.csu.edu.cn>
Date: Mon, 17 Apr 2017 16:05:07 +0800 (GMT+08:00)

Dear Professor:

   When I calculate the solvation free energy of Ni2+ in water using sander using two-step thermodynamic integration(TI) method.The first step was perturbing nothing to the metal atom Ni(with no charge) in water using the soft-core potential. Then the problem is how I setup the model of nothing in water.

If I addAtomType NO(with zero MASS,zero charge,zero Non-bonded),whether the atomtype No means nothing?

Your any reply will help me a lot.Thanks in advance. 


--
All the regards,
Jinpeng Yang
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Received on Mon Apr 17 2017 - 01:30:03 PDT
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