[gmx-users] Force field choosing and parameterization

[Gustavo Avelar Molina]

Hi,

I'm new here and I barely have experience in GROMACS. I'm seeking some help
to solve an issue.

I want to run MD simulations of an enzyme that:

1 - Have a fluorescent probe attached next to the catalytic site;
2 - Have a polysaccharide (substrate) embedded in its catalytic site;

One simulation with both conditions at the same time, another with just the
first. I don't know yet if I'll need to use a QM/MM method. Maybe you could
help me to decide it too.

The objective is to correlate the MD simulations results to other
experimental results, such as fluorescence spectroscopy of the same system,
since the fluorophore emission spectrum changes in the presence of
substrate. By knowing the probe environment changes due to the substrate
presence in comparison to the system without it, one could explain the
experimental data, and vice versa. What I want to know is:

1 - Which force field would fit well on this system?
2 - Should I develop new parameters? If so, how can I properly do it?
3 - I've heard that I should develop new parameters considering the excited
state of the fluorophore. Is it really needed?

I think that's all for now.

Thanks.


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Gustavo Avelar Molina, B.Sc. Chem.

M.Sc. Chem. Student



Departamento de Química

Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto

Laboratório de Bioquímica e Biofísica de Proteínas

Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil



+55 16 994311221 | +55 11 949874141

avelarmolinagustavo at gmail.com | gustavoavelarmolina at usp.br

https://lbbpusp.wordpress.com/o-grupo/membros/gustavo/ |

https://www.researchgate.net/profile/Gustavo_Avelar_Molina

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