[gmx-users] how to generate force field for carboxylated lysine?

[Seera Suryanarayana]

Dear gromacs users
I have a protein which has carboxylated at N epsilon position of Lysine. I
have gone through the many force fields and I did not find any force field
which represents the carboxylated lysine. Then I got the topology file for
carboxylated lysine ATB server. Now I have many questions in order to use
this topology file.

Firstly, how can I use this topology file. Do I need to add this topology
file to the pdb2gmx force  field?

Secondly, can I add the atom types and other bonded and nonbonded
information to existing force field files such .rtp, .atp and other files?

Thirdly, do I need to add the geometry file my pdb file which is being
simulated?

I am lo
Surya
Graduate student
India.