normal HEME group

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10 years 8 months ago #2565 by dariush
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Hello All,

About a year ago some people here mentioned they work to develop the HEME MARTINI FF parameters.
Is there any news?

It would be very useful for me. The approach to develop those parameters also should be interesting.

Regards,
Dariush

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10 years 8 months ago #2573 by xavier
Replied by xavier on topic HEME group
Yes we did parameterise the HEME for martini. We are still testing it and a paper is under preparation for some time already.

You should be able to find the description of the procedure in the PhD thesis of Djurre de Yong at the following link.

Then when using the HEME or other large ring molecules you have to be aware that you need to retrain its environment in the protein to avoid large deviations from the Xray structure. The ring is way too large or thick to fit in the protein cavity.

link to the thesis:
dissertations.ub.rug.nl/faculties/science/2013/d.h.de.jong/

dariush wrote: Hello All,

About a year ago some people here mentioned they work to develop the HEME MARTINI FF parameters.
Is there any news?

It would be very useful for me. The approach to develop those parameters also should be interesting.

Regards,
Dariush

Please Log in or Create an account to join the conversation.

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10 years 8 months ago #2593 by dariush
Replied by dariush on topic HEME group
Thank you! It is great!

I will try it for my protein and will share you the results.

Regards,
Dariush

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10 years 8 months ago #2599 by xavier
Replied by xavier on topic HEME group
Yes, please let us know what goes wrong :)) You might notably see the environment of the HEME deform. Additional distance restrains between the nitrogens of the HEME and the ligand(s) might help.

dariush wrote: Thank you! It is great!

I will try it for my protein and will share you the results.

Regards,
Dariush

Please Log in or Create an account to join the conversation.

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