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
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 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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