AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine

From: tonglei <>
Date: Thu, 12 Apr 2007 15:13:34 +0800

Dear Sir,
       Here is a problem confused me long time. I have simmulated a
protein-ligand complex.There is a nonstandard guanidine group in the small
molecule. CH-CH
                          / \
                        HN NH
                         \ //
   After simmulations, I found that the hydrogen atoms left the original
   Other warm-hearted man give me some helpful suggestion to add DIHE
parameters in the frcmod files, just as those in the Arg residue.
 Unfortunately, the hydrogen atoms also deviate away to some extent. I think
there maybe some difference between the nonstandard guanidine and Arg
   Here I think the IDIVF and PK value is very important, but I am not very
clear about the IDVF value of this nonstandard guandine.

  Thank you very much

Na Zhang
Chemistry Department
Zhejiang University PRC
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Received on Sun Apr 15 2007 - 06:07:16 PDT
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