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 ________________________________________________________________ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php