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

Mauricio Pablo Sica msica at unq.edu.ar
Wed Jul 18 00:03:56 CEST 2007

Dear gmx-users

I think that I have found an error in the files ffG53a(5 and 6).rtp 
related to ACE topology. Maybe it is a trivial error, but I’m sure 
someone of you will ponder it much better than me.

I am constructing the topology for an N-acetylated 2-amino sugar (N-
acetylgalactosamine) using the parameters for ffG53a5. For doing so, I 
retrieved the parameters from ffG53a6bon.itp. According to this file, I 
considered that bond parameters for an acetyl group bonded to an N atom 
should be:

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

With respect to 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 rtp file. For this group, in 
ffG53a6.rtp, the parameters are as follow:

[ bonds ]
  C    CA   gb_27
  C     O   gb_5
  C    +N   gb_19 (This is the subject of this message)

The problem is that, 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?

In fact, 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 as:

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

In addition, 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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