AMBER Archive (2009)

Subject: [AMBER] apbs-amber

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Tue Sep 22 2009 - 17:58:40 CDT

Hi amber users,

When I used apbs to calculate the binding energy between my protein and its ligand, I found the energy value change greatly with the value of the Grid box. So, now I thinks there may be some problem on my calculation. So I want to know, how amber do this job(to adjust the grid-box for different kind of  complex with different size)?

(       dime 65 97 129
       cglen 97.5 145.5 193.5
       fglen 65 97 129
       cgcent mol 1
       fgcent mol 3)

Thanks for your help in advance?

Rilei Yu

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