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From: helden%!at!%gaucho.ucsb.edu (Gert von Helden)
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Subject: AMBER parameters for non prot. arginine ?
To: chemistry- at -ccl.net
Date: Tue, 8 Nov 1994 14:10:16 +22305458 (PST)
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Hi everybody
We are doing gas phase conformational studies on small protonated peptides. The
peptide we started with is Bradykinin. Unfortunately, this peptide has two
Argininegroups in it. Since we deal with only singly protonated species,
only one arg sidechain is protonated. I looked into amber and there are no
parameters for argenine with a non protonated sidechain (which makes sense,
since they will be always protonated in solution). So my questions are:
a) Did anybody calculated parameters for non protonated arg.
b) Are there any standard AMBER atomtypes that could be used for the

    -C=N-H
     |
     NH2
   
   end of the sidechain, so that the only thing to do would be to 
   calulate charges?

Thanks for any help,  Gert

  
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 +
+ Tel   : 805-893-2673, Fax   : 805-893-8703                         +
+ E-mail: helden:~at~:gaucho.ucsb.edu                                     +
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