[gmx-users] Force field choosing and parameterization

[Gustavo Avelar Molina]

Hi, Leandro

Thanks for your explanation and tips. It helped me a lot.

Initially, I'll try to do the parameterization for the fluorophore and
substrate using GAFF and Antechamber, and then combine it with the AMBER
forcefield. After that, I'll apply this new forcefield to carry out the MD
simulations.

About the excited state issue, I don't know about its relevance yet, but I
intend to check it out when I have more time.

Sincerely,

Gustavo

==================================================
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

==================================================


2015-03-13 13:44 GMT-03:00 Leandro Bortot <leandro.obt at gmail.com>:

> Hi,
>
>      If your main interest is to correlate simulation data with
> fluorescence spectroscopy experiments I suppose the best way is to run ab
> initio calculations of the fluorescence spectra using quantum chemistry
> softwares such as Gaussian or ORCA.
>      The way I see it, the role molecular dynamics simulations can play in
> this is by allowing some refinement by explicitly introducing the system
> flexibility in your calculations and/or by considering how the solvent
> arranges itself around the fluorophore. In other words, you can run several
> ab initio fluorescence calculations using information from different frames
> of the MD simulations.
>      I believe you can't get the fluorescence information you want
> "on-the-fly" using QM/MM, since such calculations can take quite some time,
> but anyway I don't think it is necessary in your system.
>
>
>
>      1) My personal choice is AMBER99. I believe any recent version of the
> AMBER or CHARMM forcefields are well suited. I don't know about the other
> ones.
>
>      2) Yes, you will need to build the parameters for your fluorophore and
> for your substrate, unless you can find them in the literature (which, by
> the way, can be a reason to chose one forcefield over the others). For
> AMBER you can use GAFF and Antechamber. For CHARMM you can use the
> CHARMM-GUI server, but I have never tried this one by myself.
>
>      3) If the lifetime of the excited state of your fluorophore is
> relevant to the time scales sampled by molecular dynamics simulations, then
> it would necessary if such excited state affect the protein behavior and/or
> substrate binding.
>
>
>
> I hope it helps,
> Leandro
>
>
>
>
> On Thu, Mar 12, 2015 at 1:08 AM, Gustavo Avelar Molina <
> avelarmolinagustavo at gmail.com> wrote:
>
> > 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.
> >
> >
> > ==================================================
> >
> >
> >
> > 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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