[gmx-users] Carboxylate OPLS-AA parameters

rankinb rankinb at purdue.edu
Sat Jan 25 20:27:50 CET 2014

Thanks for that information.  The problem I am encountering is that the sum
of the charges of the carboxylate ion are not summing to -1.  Below is a
list of OPLS-AA parameters, including a description of the atom type and
charge.  Assume I am trying to make a topology file for butanoate.  The
number of each atom is specified, as well as the total charge for each type
of atom.  The charge on the terminal methyl group adds up to -0.1 and the
charge of the COO- head group is -0.9.  Thus, if this is correct, the charge
on the CH2 groups would need to add up to 0.  I think the problem may be
that I am using the wrong parameters of the hydrogen atoms (alkane H).  Does
anyone have any suggestions as to where I am going wrong?

	       charge      description	number	tot. charge
opls 140	0.060	        alkane H	7	        0.420
opls 271	0.700	        C in COO-	1         	0.700
opls 272   -0.800	        O in COO-	2	      -1.600
opls 273   -0.280	        C in CH3	1	      -0.280
opls 274   -0.220	        C in CH2	2	      -0.440

Purdue University 
Department of Chemistry
Ben-Amotz Research Lab
PhD Candidate

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