Subject: Guanidinium carboxylates

From: [email-masked] (Steve Bowlus)
Date: Tue, 25 Jan 94 18:13:37 -0500

1.  In MM, there are several ways to treat hydrogen bonds, and some of 
these do not give physically/biologically "real" models, although the 
energies work out fine.  For instance, Sybyl's treatment of the HB is (I 
believe) purely electrostatic, with no directionality at all.  So an 
argininium carboxylate can have all manner of geometries, so long as at 
least one N-H--O distance is reasonable.  I address the problem by 
constraining the system to a desired (biologically reasonable ?) geometry.
But this may just give me garbage, since I've told the forcefield that is
what it is to produce.  One might examine (or ask the vendor's tech support
) how the HB is modeled in the software.

2.  At the semi-empirical level, I have gotten some truly wonderful geom-
etries. . .I wonder where they came from.  Full relaxation of a guanidin-
ium carboxylate has given everything from the "standard model" hydrogen 
bonds, to systems in which the guanidinium is concave, and the carboxylate 
points into this dish (this latter with AM1).  In this case, we decided a
lysine would do just as well for the model we were developing. . . 

sb

===========================================================================
  Stephen B. Bowlus                       Computer-Aided Molecular Design 
                                          Research Division
  e-mail: [email-masked]               Sandoz Agro, Inc.
  Phone:  + 1 415 354 3904                975 California Ave.
  Fax:    + 1 415 857 1125                Palo Alto, CA 94304
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