I want to derive parameters for Ser-PLP (see attachment). For this first, I tried CGenFF web site and got a really high penalty. Also, it failed to identify the Imine bond (C=N). And gave N atom type of NG311. I have used PDB as well as mol2 with connectivity information.
With one of the advices I received from an earlier post (https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=37536#Post37536
) I tried using parameters from analog compounds as much as I can.
For pyridinium, I was able to find parameters from two places. (1) 3-hydroxypyridine and ethylpyridine from toppar_all36_prot_pyridines.str, and also from all36_cgenff.rtf for protonated pyridine (CG2R62). I am planning to derive charges and other parameters for these compounds. However, what atom type would be most reasonable to take out of these two options. In 1st option, I dont have the protonated version. But in the second option I dont have other substituents. Any assistant is highly appreciated.