AMBER Archive (2006)

Subject: AMBER: bond parameters for positively charged guanidine group

From: Ye Mei (
Date: Wed Mar 08 2006 - 20:54:15 CST

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
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

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