AMBER Archive (2007)

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

From: tonglei (xbcdnana_at_gmail.com)
Date: Thu Apr 12 2007 - 02:13:34 CDT

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
                         \ //
                           C
                            |
                           NH2
   After simmulations, I found that the hydrogen atoms left the original
planar.
   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
residue.
   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
xbcdnana_at_gmail.com

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