[gmx-users] ACE parameter error in ffG53a5-6?

Mauricio Pablo Sica msica at unq.edu.ar
Wed Jul 25 15:52:26 CEST 2007

Dear all

sorry for being here the 3rd time with this same (maybe trivial) 

I have found what appears to be an error in the files ffG53a(5 and 6).rtp 
related to the ACE group topology. Maybe it is a trivial error, or a 
change due to something I am missing. 

I was constructing the topology for N-acetylgalactosamine ffG53a6 
parameters. In general, my strategy was to acetylate a 2-amino galactose.
According to data in ffG53a6bon.itp, “my” acetyl group bonded to the 
sugar amino should have:

[ bonds ]
  CA  C   gb_27
  C   O   gb_5
  C   N   gb_10 ; parameter for the peptide (amide) bond.

I choose gb_10 according to ffG53a6bon.itp, where:

     #define gb_10       0.1330  1.1800e+07
     ; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)       1000    

The problem arose when I compared what I did to the ACE group in the 
ffG53a6.rtp. There I found that:

[ bonds ]
  C    CA   gb_27
  C     O   gb_5
  C    +N   gb_19; <<<<  (Here is the discrepancy)

According to ffG53a6bon.itp, gb_19 is a CHn-O bond, as you can see:

     #define gb_19       0.1430  9.2100e+06
     ; CHn  -  OM    900     

Could it be an error or the choice is due to something I am missing?

Additionally, in the force fields 43a1, 43a2, 43b1 and 45a3, the 
parameter for the said C-N bond is gb_9, which in all cases is defined as:

     define gb_9        0.1330  1.1800e+07
     ; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)       1000

Also, in ffG53a6.rtp, "C +N" bonds are gb_10 for all residues, except for 

The question, again, is: is gb_19 correct? If yes, please tell me why.

Sorry for the length of the mail and thanks for your attention.


Dr. Mauricio P. Sica                    LEPP
Phone: (54011)4365-7100 ext. 169        Laboratorio de Expresión
R. Saenz Peña 354                       y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires         Universidad de Quilmes

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