In Amber, you use different atom types for your C's and N's in each
situation, rather than specifying bond orders. I am not chemist enough
anymore to name the atom types involved, but if you can find them here
(quick link, not sure if best FF), you likely are in luck.
https://github.com/Amber-MD/pymsmt/blob/master/lib/parm10.dat
If not, you will need to define new atom type(s), or possibly use or
borrow from the gaff force field.
In any case, you will have to define residue templates for each
situation using the different atom types, and derive charges for them,
likely referencing how the charges were done for the residues involved
in disulfide bonds.
Bill
On 9/28/16 1:43 AM, Ming Tang wrote:
> Dear list,
>
> I want to study protein with crosslinks (deH-LNL and HLKNL) in amber. These crosslinks form between Lysine/hydroxylysine and Lysine residues, and have R-CH=N-R' or R-CH2-NH-R' functional groups. Could anybody tell me whether amber can handle C-N and C=N bonds just like disulphide bonds?
>
> Thank you,
> Ming
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Received on Wed Sep 28 2016 - 03:00:02 PDT
