normal Looking for charmm AA cholesterol structure matching backward map file

  • cneale
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4 years 3 months ago #8471 by cneale
Hello,

does anyone have a cholesterol structure file that corresponds to the CHOL.charmm36.map atom order here: cgmartini.nl/index.php/force-field-param...r=Sterols&lipid=CHOL ?

The charmm-gui uses different cholesterol atom names, and I'd like to update my CHOL.charmm36.map file so that it works with the charmm-gui output.

Thank you,
Chris.

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4 years 2 months ago #8475 by poojaric
Hi,

I just prepared CHOL.charmm36.map file which corresponds to the charmm-gui generated AA cholesterol structure file. I was able to backmap the membrane and run initial minimization without any issues. If you require the file I can share with you.

Kind Regards,
Chetan

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4 years 2 months ago #8476 by riccardo
Great. Maybe it's a good idea to add it to the Backward's Mapping directory on GitHub ( github.com/Tsjerk/Backward ), as it may be useful to other people. You could do that via a pull request.

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3 years 6 months ago #8784 by slall
Hello Chetan,

Could you please share the mapping file that you have created? I am trying to map cholesterol from martini to atomistic representation and have not been successful so far.

Thanks in anticipation.

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3 years 6 months ago #8785 by poojaric
Hi,

Sure. I dont see an option to attach the file here. If you could write to me (This email address is being protected from spambots. You need JavaScript enabled to view it.) I can send you the files.

Kind Regards,
Chetan

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1 year 4 months ago #9583 by moon
Hi
I am also searching for a mapping file with the correct order from charmm-gui. Can you kindly share it?
Thanks a lot

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