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  5. CG Coordinates for Cholesteryl oleate and POPC

normal CG Coordinates for Cholesteryl oleate and POPC

  • bt12d026
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11 years 2 months ago #1398 by bt12d026
CG Coordinates for Cholesteryl oleate and POPC was created by bt12d026
Dear all,
I am a newbie to MARTINI. I have downloaded the forcefield parameters for cholesteryl oleate (CE) and POPC from Martini website. I don't know how to convert an all-atomic pdb to CG for the same. Is there any script (like martinize.py for proteins) for lipids for conversion? Please help me in this regard. By chance, If somebody have the CG coordinate files, Please provide. Thanks for your valuable time.

Cheers,
Venkat

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11 years 2 months ago #1399 by djurre
Replied by djurre on topic CG Coordinates for Cholesteryl oleate and POPC
You can try to start from a lipid that has a similar number of beads and thourougly minimize it (start using conjugate gradient). That will probably give you a a proper starting structure.

Later this week I'll try to put online a script that generates a structure starting from an input itp. The script pretty much uses the above method.

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11 years 2 months ago #1400 by bt12d026
Replied by bt12d026 on topic CG Coordinates for Cholesteryl oleate and POPC
Thank you djurre for the nice suggestion. Eagerly waiting for the script. Thanks alot

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10 years 11 months ago #1558 by djurre
Replied by djurre on topic CG Coordinates for Cholesteryl oleate and POPC
It took a bit longer then I promised, but the script to create molecular stuctures starting from a top/itp has been put online. It is called molmaker.py and can be found under "downloads>>tools":
http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/266-molmaker

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  1. Force Fields
  3. Lipids
  5. CG Coordinates for Cholesteryl oleate and POPC
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