normal backmapping of Cholesterol molecule from CG model to atomistic

  • shwetaa7
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4 years 7 months ago - 4 years 7 months ago #8227 by shwetaa7
I have Martini coarse-grained model of protein in complex with cholesterol. I have followed the backmapping tutorial ( md.chem.rug.nl/index.php/tutorials-gener...others-gmx5#Backward ). Now, I am trying to backmap my system (protein-cholesterol), it does not work. It works for protein only.

I am using the charm36 forcefield, and the initram-v5 script for backmapping.

For cholesterol it says:
Checking dependencies:
backward.py ... Missing dependency: backward.py

Thanks in advance
Last edit: 4 years 7 months ago by shwetaa7.

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4 years 6 months ago #8240 by riccardo
This error really means just that "initram.sh" cannot find "backward.py", that is, backward.py is not in the same folder where you run initram.sh. So, I wouldn't believe that the same script in that same folder would manage to backmap the protein-only system but not the protein+cholesterol. Maybe you created a new folder and forgot to copy paste also "backward.py" in there?

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