[gmx-users] special bond

[fantaman]

Dear Justin,

thank you very much for your help!! Indeed it helped me fixing the problem!!

Could I ask you also a brief question about special bonds? I have defined in
specbond.dat a special bond between 2 atoms, say ATM1 & ATM2, of 2 different
residues but belonging to the same chain, like this:

1
RES1	ATM1	1	RES2	ATM2	1	0.288	RES1	RES2

and afterwards I have defined in ffbonded.itp the bond gb_99 like this:

#define gb_99     0.288     3.0402e+07
; ATM1 - ATM2 special bond

and then at the end of the same file I have written down:

; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
ATM1   ATM2    2    gb_99

By doing so, then pdb2gmx runs nicely but in the speptide.top file I do get
in the [ bond ] section all the couples of ATM1 & ATM2 atoms, but no gb_99
bond is there... Would you have any clue why? I have read that too strong a
coupling constant might cause problems and I have therefore tried with a
normal one, but still no gb_99 is there...

Thank you very much in advance,

Nicola

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