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
Argentina
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