[gmx-users] Force field choosing and parameterization

[Leandro Bortot]

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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