[gmx-users] ffbonded.itp file

anna.marabotti at isa.cnr.it anna.marabotti at isa.cnr.it
Tue Apr 5 19:49:11 CEST 2011

Dear gmx-users,
I’m 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
;       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 don’t
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 don’t
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. I’m
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 don’t 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

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