[gmx-users] ACE group parameter error un ffG53a5-6?

Mauricio Pablo Sica msica at unq.edu.ar
Wed Jul 18 16:35:16 CEST 2007

Dear all

Sorry for repeating this message. 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’m sure you experts will ponder it much better than me.

I was constructing the topology for N-acetylgalactosamine using the 
parameters for ffG53a5. In general, my strategy was to acetylate a 2-
amino galactose. So, considering the parameters from ffG53a6bon.itp, the 
acetyl group bonded to the NH of the sugar was:

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

In particular, for the C-N bond, I choose gb_10 according to its 
definition in ffG53a6bon.itp:

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

The problem arose when I wanted to compare what I did to what is 
parameterized for 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 defines parameters for C-O bonds, 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 
parameters for the said C-N bonds are gb_9, which is in all cases defined 

     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 paremeterized according to gb_10 
for all residues except for ACE, which has one of the three gb_19 in the 
file (although I know that these statistics are not sufficient for 
dismiss the choice for gb_19).
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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