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normal Looking for charmm AA cholesterol structure matching backward map file

  • cneale
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4 years 1 month ago #8471 by cneale
Looking for charmm AA cholesterol structure matching backward map file was created 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 1 month ago #8475 by poojaric
Replied by poojaric on topic Looking for charmm AA cholesterol structure matching backward map file
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 1 month ago #8476 by riccardo
Replied by riccardo on topic Looking for charmm AA cholesterol structure matching backward map file
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 4 months ago #8784 by slall
Replied by slall on topic Looking for charmm AA cholesterol structure matching backward map file
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 4 months ago #8785 by poojaric
Replied by poojaric on topic Looking for charmm AA cholesterol structure matching backward map file
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 2 months ago #9583 by moon
Replied by moon on topic Looking for charmm AA cholesterol structure matching backward map file
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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