[gmx-users] Constraint bonds

[rose rahmani]

Hi,

I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond,
Mn-O bond,... formed. Now i want to do MD simulation for this
functionalized nanotube. (I use AMBER99SB ff)

How should i define ffbonded.itp?I have bond length and angles but i don't
know kb. If for example kb of Mn-O for another similar structures exists in
literatures can i use them?
If kb doesn't exist, can i freeze this BOND(not the whole AA) on known bond
length, ANGLE on known dihedral angle and known partial charges charges(all
achieved after functionalization of NT with AA by DFT) or maybe constraint
it?
Is it possible to freeze bond at all?! Is there any better choice?


Would you please help and correct me?

Best regards