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Increasing Protein-Water Interaction Strength & martinize.py
- nkho
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2 years 4 months ago #9078
by nkho
Increasing Protein-Water Interaction Strength & martinize.py was created by nkho
Hello,
I recently got some coarse grained simulations working with martini_v2, and then found out v3 was much more accurate and came out recently.
Downloaded the martini v3 package from here:
cgmartini.nl/index.php/martini3beta
I imagine there must be a more updated version? Anyways, I have two questions. Firstly, I would like to modify the interact strength of protein-water interactions as I'm running IDP simulations and this has been found to decrease the compactness of the protein in the simulation.
I opened up martinize_v3.0.b.3.2.itp and modified all of the interactions involing WN beads (except WN-WN), and multiplied epsilon (last column?) by 1.06 for a 6% increase in well depth... is this the right way to do this?
Secondly, the martinize script is broken for me. I cannot convert to coarse grain with martini 3, this is the error I get:
Does anyone have a working version of the martini 3 coarse grain mapper python script?
Thank you!!
nkho
I recently got some coarse grained simulations working with martini_v2, and then found out v3 was much more accurate and came out recently.
Downloaded the martini v3 package from here:
cgmartini.nl/index.php/martini3beta
I imagine there must be a more updated version? Anyways, I have two questions. Firstly, I would like to modify the interact strength of protein-water interactions as I'm running IDP simulations and this has been found to decrease the compactness of the protein in the simulation.
I opened up martinize_v3.0.b.3.2.itp and modified all of the interactions involing WN beads (except WN-WN), and multiplied epsilon (last column?) by 1.06 for a 6% increase in well depth... is this the right way to do this?
WN WN 1 4.700000e-01 4.650000e+00 #unmodified
WN P4 1 0.470 5.744270 #epsilon increased by 6%
WN P2 1 0.470 5.428651 #epsilon increased by 6%
WN P1 1 0.470 5.176156 #epsilon increased by 6%
WN N3 1 0.470 5.176156 #epsilon increased by 6%
WN N1 1 0.470 4.671165 #epsilon increased by 6%nick@Desktop:~/GROMACS/projects/CG-3$ ./martinize
Traceback (most recent call last):
File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "./martinize/__main__.py", line 3, in <module>
File "<frozen zipimport>", line 259, in load_module
File "./martinize/martinize/__init__.py", line 37, in <module>
ModuleNotFoundError: No module named 'core'Does anyone have a working version of the martini 3 coarse grain mapper python script?
Thank you!!
nkho
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- riccardo
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2 years 4 months ago #9092
by riccardo
Replied by riccardo on topic Increasing Protein-Water Interaction Strength & martinize.py
Those Martini 3 parameters are for the open-beta version. The final parameters have been released recently, you can find them here:
cgmartini.nl/index.php/martini-3-0
Make sure to read the publication. Plenty of info can be found in the SI.
You should use martinize2 to build Martini 3 systems: github.com/marrink-lab/vermouth-martinize . More detailed tutorials are coming, but via this forum and the github issues you should be able to get started.
Note that Martini 3 improved considerably over the "sticky" proteins problem. If you want to play with W-W interactions (in the final release, water is called again "W") OK - but mind that that will mess with the overall balance of the force field. I'd give a shot to Martini 3 first. Very good results have been obtained for protein-protein interactions in different environments (see, e.g., Figure 3 of www.nature.com/articles/s41592-021-01098-3 ).
Make sure to read the publication. Plenty of info can be found in the SI.
You should use martinize2 to build Martini 3 systems: github.com/marrink-lab/vermouth-martinize . More detailed tutorials are coming, but via this forum and the github issues you should be able to get started.
Note that Martini 3 improved considerably over the "sticky" proteins problem. If you want to play with W-W interactions (in the final release, water is called again "W") OK - but mind that that will mess with the overall balance of the force field. I'd give a shot to Martini 3 first. Very good results have been obtained for protein-protein interactions in different environments (see, e.g., Figure 3 of www.nature.com/articles/s41592-021-01098-3 ).
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