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Info on combined use of the Martini 3 force field and Go̅-like models
- moon
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2 years 11 months ago #8934
by moon
Info on combined use of the Martini 3 force field and Go̅-like models was created by moon
Dear all
Thanks for the useful tools and help that you are providing.
I'm interested to test on my protein/membrane system the combined use of MARTINI 3 with a Go̅-like model to have fewer limitations on the protein conformational flexibility, as used in this nice recent publication doi.org/10.1021/acs.jcim.1c00261 . I was wondering which is the best approach, and steps to follow, to use martinize2/martini 3 in combination with a Go̅-like model.
Best regards
Thanks for the useful tools and help that you are providing.
I'm interested to test on my protein/membrane system the combined use of MARTINI 3 with a Go̅-like model to have fewer limitations on the protein conformational flexibility, as used in this nice recent publication doi.org/10.1021/acs.jcim.1c00261 . I was wondering which is the best approach, and steps to follow, to use martinize2/martini 3 in combination with a Go̅-like model.
Best regards
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- sebastian
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2 years 11 months ago #8953
by sebastian
Replied by sebastian on topic Info on combined use of the Martini 3 force field and Go̅-like models
Hi,
We are working on a new version of the script. Its beta-release will be announced on the Martini website - so stay tuned.
Best,
Sebastian
We are working on a new version of the script. Its beta-release will be announced on the Martini website - so stay tuned.
Best,
Sebastian
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- bart
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2 years 11 months ago #8954
by bart
Replied by bart on topic Info on combined use of the Martini 3 force field and Go̅-like models
Good nieuws! I am tuned :D
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- jlillard
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2 years 10 months ago #8971
by jlillard
Replied by jlillard on topic Info on combined use of the Martini 3 force field and Go̅-like models
The martinize2.py script contains an option (-govs-includes) for using "Virtual site-based GoMartini." Running martinize2 with this option produces the following note:
INFO - general - The output topology will require files generated by "create_goVirt.py".
Is the virtual-site GoMartini method still useful/valid, or has it been deprecated; and if it is still valid, where can "create_goVirt.py" be found?
INFO - general - The output topology will require files generated by "create_goVirt.py".
Is the virtual-site GoMartini method still useful/valid, or has it been deprecated; and if it is still valid, where can "create_goVirt.py" be found?
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- riccardo
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2 years 10 months ago #8997
by riccardo
Replied by riccardo on topic Info on combined use of the Martini 3 force field and Go̅-like models
Please see comment above of Sebastian. "create_goVirt.py" is the script Sebastian referred to in the post above.
Current versions of the script can be found at: info.ifpan.edu.pl/~panos/panos/GoMartini.html / cgmartini.nl/index.php/go-martini-development
Current versions of the script can be found at: info.ifpan.edu.pl/~panos/panos/GoMartini.html / cgmartini.nl/index.php/go-martini-development
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