[gmx-users] how to fit parameters for terminal residues in amber99sb-ildn?

[sang eun jee]

Dear  gromacs users

Hello. I have question how to decide terminal residue forcefield and put
them in library?

I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or opls
forcefield, amber forcefield treat termini in its own way and current
version only works with NH3+ and COO-. I would like to termini as a neutral
status, NH2 and COOH and would like to modify forcefield to include this
specific termini data.

To decide charges and parameters to describe specific termini, is there any
way to decide parameters based on non-terminal residue database? When I
looked at NGLY and GLY from animoacids.rtp,  I could not find out specific
rules.

Thank you very much.

Sangeun Jee
-- 
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology