Hello Leon,
I worked in a small molecule parametrization, just of its bonded terms, and
experienced a lot of trouble. It involved a silicon portion, so, i couldn't
find easily this parameters to use in AMBER.
Six months later, I finally obtained a good parameter set, using Paramfit
for fitting only constants, using equilibrium parameters from QM
calculations (I used another programs/metodologies, that didn’t work out in
my case).
It was really difficult because I started learning about parametrization
from scratch, and there is not a great amount of literature about it to
fall back on.
I don't know what system do you wanna parametrize, but, if you need bonded
terms, start doing Paramfit tutorial (
http://ambermd.org/tutorials/advanced/tutorial23/paramfit_lite.html).
During this months, I wrote a script that helps in all parts of this
tutorial and has a few other useful tools, making the job more easy. I'm
adjusting a few last things in the code (finishing to add some
functionalities), and I will publish at github. Maybe this can help you
too.
If you start working in something like that, you can email me. If I can
help in something, I’ll gladly do.
Good Luck and best wishes
Em seg, 27 de ago de 2018 às 10:03, Leon Hardy <leonhardy.mail.usf.edu>
escreveu:
> Does anyone know the best method or practices when parameterizing drugs,
> ligands or metal ions bound to protein? Which parameter files?
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--
Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
GE
⎜
EM
〉
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – Brasil*
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Received on Mon Aug 27 2018 - 09:30:02 PDT
