Dear all
sorry for being here the 3rd time with this same (maybe trivial)
question.
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
ACE.
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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