Dear gmx-users, Im trying to modify the ffbonded.itp file of Gromos43a1 ff in Gromacs 4.5.3 version, in order to add parameters for my modified Cys residue. However, I have some difficulties in understanding what are the parameters already included in this file. In particular, ffbonded.itp file appears as:
; Table 2.5.2.1 ; GROMOS bond-stretching parameters ; ; ; Bond type code ; Force constant ; Ideal bond length ; Examples of usage in terms of non-bonded atom types ; ; ; ICB(H)[N] CB[N] B0[N] ; #define gb_1 0.1000 1.5700e+07 ; H - OA 750 ; #define gb_2 0.1000 1.8700e+07 ; H - N (all) 895 ; #define gb_3 0.1090 1.2300e+07 ; HC - C 700 .................................... but while I understand the meaning of the first two numbers, I dont understand what the number near the description of the two atom type is (for example, in the definition of gb_3, what is 700 after HC C? I looked at the Manual of Gromacs version 4.5.3, section 5, paragraph 5.3.3. Bonds (page 111) but the example excerpt for ffbonded.itp file is very different from the one I see in my ffG43a1 directory! I dont see in the manual or elsewhere a detailed explanation for the meaning of each component of this file. Could you please help me? Moreover, I see some strange definitions, at least in my opinion. Im trying to mutuate parameters from DMSO: (CH3)2S=O. Under the section Bond type, I see these definitions: #define gb_44 0.280412 2.3900e+06 ; ODmso - CDmso 900 ; #define gb_45 0.292993 2.1900e+06 ; CDmso - CDmso 900 I really dont understand the sense of the definition of these bonds types, provided that they are absent in DMSO since the two methyl groups are linked only to sulphur, not to each others (no C-C bond) and that oxygen is linked only to sulphur (no O-C bond). Could you please check for these strange interactions, or am I mistakenly interpreting them? Thank you very much and best regards Anna Marabotti -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
