normal Backward failed for CHOL molecules

  • Smotta
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2 weeks 2 days ago #7414 by Smotta
Smotta created the topic: Backward failed for CHOL molecules
Hi,

I'm trying to backmap a Martini CG system composed of two proteins, within a membrane of POPC/CHOL 10:1. While the backmapping works with proteins only, it failed when I try to backmap the whole membrane. In particular I obtain an initial warning for cholesterols:
Not all positions defined for [trans] operation:
[('C44', None), ('C47', None), ('C1', (8.931246084195303, 3.4044965661932687, 4.687000913633694)), ('O2', None)]
Not all positions defined for [trans] operation:
[('H45', None), ('C47', None), ('C1', (8.931246084195303, 3.4044965661932687, 4.687000913633694)), ('O2', None)]
Not all positions defined for [trans] operation:
[('H46', None), ('C47', None), ('C1', (8.931246084195303, 3.4044965661932687, 4.687000913633694)), ('O2', None)]

After that those warnings, the initram.py script launch energy minimizations completed and MD simulations, but at the first step of MD, the simulation stopped due to LINCS warnings. Even trying to increase minimization steps or reduce simulation timestep failed.
The problem appear to be related to CHOL molecules because removing them from the system the simulation initram pipeline works and the final structure (without cholesterols) looks fine.

The backmap of a single CHOL molecule was instead completed properly.
How can I resolve the problem?

PS: I used the charm36 forcefield, and the initram-v5 script for backmapping.

Thanks!

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1 week 3 days ago #7417 by riccardo
riccardo replied the topic: Backward failed for CHOL molecules
Hi,

do you get the same warning when you try to backmap a single CHOL?
How big is your system?

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1 week 3 days ago #7418 by Smotta
Smotta replied the topic: Backward failed for CHOL molecules
Yes, I get the same error when I backmap a single cholesterol molecule. My system us a 20×20 membrane POPC:CHOL 10:1 with 2 proteins embedded.

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1 week 3 days ago #7419 by riccardo
riccardo replied the topic: Backward failed for CHOL molecules
Looking through the forum, the error you get seems to be similar to this one:

www.cgmartini.nl/index.php/component/kun...-backward-py-mapping

(see the last three posts). Please let me know if this fixes it.

I suppose also you got the mapping file for chol from:

cgmartini.nl/index.php/force-field-param...r=Sterols&lipid=CHOL

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