normal Increasing Protein-Water Interaction Strength & martinize.py

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1 year 6 months ago #9078 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?
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%
Secondly, the martinize script is broken for me. I cannot convert to coarse grain with martini 3, this is the error I get:
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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1 year 6 months ago #9092 by riccardo
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 ).

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