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

Seera Suryanarayana palusoori at gmail.com
Mon Apr 15 12:02:19 CEST 2019

Dear gromacs users

Sorry for my previous email which has been sent by mistakenly.
Coming to my problem,

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

Kindly tell me how handle with my carboxylated residue.

Thanks in advane
Graduate student

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