AMBER: bond parameters for positively charged guanidine group

From: Ye Mei <ymei.itcc.nju.edu.cn>
Date: Thu, 9 Mar 2006 10:54:15 +0800

Dear Amber users

I am working on a drug molecule which has a positively charged guanidine group. I followed the default routine to build the parameters for this drug molecule. But after md simulation, two hydrogen atoms leave the plan of heavy atoms, which seems to be the typical -NH2 structure. I know I should modify the bond parameters, but I donot know what I should do exactly. Could anybody help me?

      
                                 
Best regards,

Ye Mei
ymei.itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2006-03-09

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Received on Sun Mar 12 2006 - 06:10:17 PST
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