[gmx-users] terminal residue

[Lakshmi Padmavathi]

Dear Gmx users,

 i want to use a protein along with an heteroatom. the heteroatom is linked to 
the protein. the terminal atom of the heteroatom is ch3. it has to link with 
lysine NH2 ( sidechain).

i am getting error in pdb2gmx. that c is not fount in 220 residue. which is my 
heteroatom residue number.

how can i solve this. hetero atom number is 220, and lysine number is 216.

how will the gromacs recognise the CH3 as terminal.

can i add this CH3 in ***_c.tdb ?

could anybody help me regarding this?

thank you very much in advance.


sincerely,