[AMBER] Parametrization: consistency with gaff force field

From: Alechania Misturini <alechaniam.gmail.com>
Date: Tue, 8 May 2018 15:25:50 -0300

*Greetings everyone,I’m parameterizing a few bonded terms of a ligand
moiety (involving a sp3 silicon atom and its neighbourhood). Reading some
books and articles about parametrization, a question has arisen about the
consistency of generated parameters with the force field employed (GAFF, in
my case).“ The consistent application of the same molecular mechanics
formalism and the same molecular orbital theory in development of the
force-field parameter data base should insure self-consistency and
reliability in the use of the resultant force field at a level near that of
the quantum mechanical method. J Comp Chem, Vol. 5, No. 5, 486-499 (1984)”*

*Looking for QM levels of theory employed, at Amber manual, as well GAFF
and RESP papers:RESP) Opt calculation: MP2/6-31G* (at an tutorial, b3lyp
was used in place of mp2, claiming similar results/less time);
           Esp calculation (single point): HF/6-31G*;GAFF) force constants
for bonds and angles: from traditional AMBER force fields;
           equilibrium bond length and angle: MP2/6-31G* and
crystallographic data from CSD; torsional terms: optimized with
PARMSCAN - Opt calculation: MP2/6-31G* ; single point MP4/6-311G(d,p);(cap
15 AMBER manual)*

*Due the silicon atom present in the fragment, I need at least a triple
zeta basis set to better describe it, so, I did a benchmark with some
functionals and basis set (MP2, B3LYP and PBE0, with 6-31G*, 6-311G*,
def2-TZVP and cc-pVTZ). Fortunately I could find a similar x ray structure
to help me validate these results, and pick the best level of theory for my

*Having in mind the consistency with the rest of force field parameters, in
case of Resp charges, for example, can I use without problems the selected
level in the benchmark to optimize the structure and use HF/6-31G* as
indicated for ESP points?*

*The same doubt rise about the structures used to parametrize with paramfit
or mdgx. Different QM level of theory than the employed in GAFF force field
can result in inconsistent parameters, looking the whole picture? (cause
just bonded parameters will be parametrized, LJ values will come from GAFF
and parm99 data, for Si)*

*There are more specific literature about it, that I didn’t find yet? Cause
I’m starting now in these research field, so, some advice about it would be
welcome!Thanks in advantage.*

Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – UFSC*
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Received on Tue May 08 2018 - 11:30:02 PDT
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