AMBER Archive (2009)
Subject: [AMBER] RESP RED
From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Fri Sep 11 2009 - 13:40:24 CDT
I am using R.E.D. to derive the charge of my molecule.
My molecule composes of two fragments, I set the total charge of my molecule to +1, charge of fragment 1 to -1, and charge of fragment 2 to +2.
After calculating charge using RESP-C1, I found the sum of partial charges on fragment 1 not equal to -1, also charge on fragment 2 not equal to +2.
Could you help me out and tell me why that happened and how I can achieve portioning the charge with setting the sum of charge on fragment 1 to -1 and on fragment2 to -2?
Also, which model do you prefer? RESP-A1 or RESP-2, or something else.
I just studying binding energy of some inhibitors inside an active site.
Thanks in advance
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