normal biotin parametrizion in martini

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10 years 6 months ago #2077 by saracino
biotin parametrizion in martini was created by saracino
Hi all,
I would like to simulate biotinylated self-assembling peptides with martini force field.
There is someone working on getting parameters for biotin/biotinyl-termination or even interested in doing it?
If you could diffuse this call and contact me it would be great.
Thanks at all,
Gloria

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10 years 6 months ago #2095 by Clement
Replied by Clement on topic biotin parametrizion in martini
Hi Gloria,

To our knowledge, nothing was done in this direction... It's a bit challenging due to the ring structures, but you could try to parameterize this type of group; do you have any AA parameters/simulations yet? What type of experimental data you can gather on these?

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10 years 6 months ago #2132 by saracino
Replied by saracino on topic biotin parametrizion in martini
Thanks for your answer Clement.
I performed some simulation of monomers, dimers, tetramers and octamers of such biotinilated peptides with 53a6 force field in gromacs: parameters already available in the force field have been used while the initial structures have been obtained by HF optimization in Gaussian (details in Modelling and analysis of early aggregation events of
BMHP1-derived self-assembling peptides
, GAA Saracino and F Gelain. J Biomol Struct Dyn 2013 dx.doi.org/10.1080/07391102.2013.790848 ).
In literature are available structural data, mainly regarding biotin-streptavidin complex; values of partition coefficient at different pH and of vaporization enthaply calculated with Advanced Chemistry Development (ACD/Labs) Software V11.02 are available on scifinder database.
Experimentally in our lab we found a great self-assembling ability in hyerarchical nanostructures that have been characterized by x-ray, FTIR, CD and rheometer.
Even if the results obtained by the simulations gave interesting insights about the assembling mechanism, begin to approach the real target exending the exploration towards coarse grained methods can be even more but I have no experience in this regard.
Any suggestions are welcome.

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10 years 6 months ago #2133 by Clement
Replied by Clement on topic biotin parametrizion in martini
If you have a bit of time to spend on the CG models/simulations, and since you already have atomistic trajectories and quite some experimental data, I'd would advice to parameterize this biotin group. It's a matter of a week or so, if all goes well; but there's always some unscheduled problems, otherwise it wouldn't be fun!
The recipe is detailed here , and many many many advises are spread all around this Forum. But you can always ask for more!

Good luck!

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9 years 3 months ago #4212 by saracino
Replied by saracino on topic biotin parametrizion in martini
Dear Martini team,
I know it's been a bit 'of time, but we are only now beginning to introduce the Biotinyl N-terminal (BTN) for peptides in the Martiniff to perform CG simulations of biotinylated self-assembling peptides. A first simple mapping on CG representation was made using bonds, lengths, angles and dihedrals extracted from our previous gromos53a6 simulations. The force constants were assigned according to other mappings shown in martini_v2.2_aminoacids.itp.
I tried to follow a standard simulation protocol (minimization in vacuum and in water&ions, a short position restrained run, NVT run and npt production run) and to compare distributions of structural parameters with corresponding ones of our previous simulations made with gromos53a6ff.
Minimizations both in water and in the water&ions seems to regularly proceed and without Lincs warnings as well as the position restrained (50 ps) and the NVT simulations (50ps).
The NPT simulation shows instead immediately Lincs warnings involving BTN atoms and the system explodes.
I don't know if it is because of a mapping oversimplified or of certain input parameters that may not be quite appropriate to a parametrization procedure. I would like that you give a look at the PDB, itp and MDP files that I used, how do you prefer that I send the files?
Any suggestions to improve our procedure is welcome,

thanks in advance,

Gloria

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9 years 3 months ago - 9 years 3 months ago #4213 by Clement
Replied by Clement on topic biotin parametrizion in martini
Hi Gloria,

I see that problems occurred indeed... I shouldn't have said that in my previous post. Hoped it didn't actually take you these 14 months to parameterize! ;-)

You can send the files to me (This email address is being protected from spambots. You need JavaScript enabled to view it. ), I can have a look at them and show them around for more advises. But you can start by giving slightly more details of this protocol, while I'm commenting on what you wrote already: you do not need to do so many steps of minimization/equilibration with the Martini FF; one minimization in solvent (500 to 2000 steps should be enough), followed by a position restrained NpT simulation - if really needed - and regular equilibration(s). Try to do at least 10 ns per equilibration cycle, CG simulations aren't expensive. If it crashes, try to run successive equilibrations with smaller time steps in between for instance. Talking about time step, what are the ones you're using in your various simulations?

Good luck,

Cl.
Last edit: 9 years 3 months ago by Clement.

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9 years 3 months ago #4215 by saracino
Replied by saracino on topic biotin parametrizion in martini
Hi Clement,
for variuos reasons, unfortunately, the parametrizations started only now.
The time step used in position restrained, NVT and NPT is 0.01 to avoid the crash. The NPT simulation crashes anyway.
I sent you the file, I hope that you will receive them.

Thank you

Gloria

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