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coordinate file for cholesterol
- yuxiang900599015
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8 years 8 months ago #4799
by yuxiang900599015
coordinate file for cholesterol was created by yuxiang900599015
Hi all,
Could someone give me a coordinate file of cholesterol corresponding to the file 'martini_v2.0_CHOL_01.itp.' I tried to build the molecule by myself, but it gives error in simulation.
Thank you
Could someone give me a coordinate file of cholesterol corresponding to the file 'martini_v2.0_CHOL_01.itp.' I tried to build the molecule by myself, but it gives error in simulation.
Thank you
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- mnmelo
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8 years 8 months ago #4808
by mnmelo
Replied by mnmelo on topic coordinate file for cholesterol
Hi Yuxiang,
The quick solution for your problem is to use the molmaker.py script we provide. It was made for exactly the cases where you want to create a structure from only an .itp:
(The -ff flag can point to whichever Martini version .itp you're using, not necessarily v2.1.)
If that still doesn't work (it does for me), or if you prefer to continue with your approach, here's a more in-depth solution:
Cholesterol topologies have underlying constraints that are hard to properly energy-minimize, and that's probably the problem you're facing. If you replace all constraints in the .itp with bonds of the same length and a very high force (1.0e6 is ok) the energy minimization algorithm will do a much better job.
Just don't forget to switch back to constraints when you're done minimizing.
Good luck,
Manel
The quick solution for your problem is to use the molmaker.py script we provide. It was made for exactly the cases where you want to create a structure from only an .itp:
molmaker.py -i cholesterol.itp -ff martini_v2.1.itpIf that still doesn't work (it does for me), or if you prefer to continue with your approach, here's a more in-depth solution:
Cholesterol topologies have underlying constraints that are hard to properly energy-minimize, and that's probably the problem you're facing. If you replace all constraints in the .itp with bonds of the same length and a very high force (1.0e6 is ok) the energy minimization algorithm will do a much better job.
Just don't forget to switch back to constraints when you're done minimizing.
Good luck,
Manel
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