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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 25 17:01:58 CEST 2007


Repeating a question like this is pointless. Apparently, people don't
know the answer just like that or are concerned with things other than
ACE. Intuitively, I'd say you're probably right, but I wouldn't dare
make any statement from it. What about the original force field papers
for the 43a2/45a3/53aX series? If these don't mention a change of such
parameters explicitly, it's likely that the parameters should still be
the same across the version, and the renumbering worked out wrongly.
Maybe try to get hold of the original GROMOS force field files from
the group of Zurich and see what's in there. AFAIK the gromacs
implementation is converted from these original files.


On 7/25/07, Mauricio Pablo Sica <msica at unq.edu.ar> wrote:
> 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 AiresUniversidad de Quilmes
> Argentina
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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