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lipidated amino acids in martini3
- poojaric
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4 years 6 months ago #8270
by poojaric
lipidated amino acids in martini3 was created by poojaric
Dear All,
Previously I was preparing lipidated protein for simulations using the martinize 2 script.
Now, I would like to repeat the simulations with the latest martinize script provided within the martini 3 package. Unfortunately I am not able to open the martinize script either in terminal or text editor to add the lipidation parameters.
Please can I know if there is version of martinize script which can be edited to include the lipidation parameters.
Kind Regards,
Chetan
Previously I was preparing lipidated protein for simulations using the martinize 2 script.
Now, I would like to repeat the simulations with the latest martinize script provided within the martini 3 package. Unfortunately I am not able to open the martinize script either in terminal or text editor to add the lipidation parameters.
Please can I know if there is version of martinize script which can be edited to include the lipidation parameters.
Kind Regards,
Chetan
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- peterkroon
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4 years 6 months ago #8272
by peterkroon
Replied by peterkroon on topic lipidated amino acids in martini3
Hi Chetan,
there's two ways forward:
1) use the -ff-dir and -mapping-dir options. These allow you to provide your own forcefield and mappings directories without having to touch those that ship with martinize2.
2) Grab the source at github.com/marrink-lab/vermouth-martinize
Note that you will get best results if your lipidation is its own residue.
HTH Peter
there's two ways forward:
1) use the -ff-dir and -mapping-dir options. These allow you to provide your own forcefield and mappings directories without having to touch those that ship with martinize2.
2) Grab the source at github.com/marrink-lab/vermouth-martinize
Note that you will get best results if your lipidation is its own residue.
HTH Peter
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- poojaric
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4 years 6 months ago #8274
by poojaric
Replied by poojaric on topic lipidated amino acids in martini3
Dear Peter,
Thanks for your quick reply and suggestions. I will work on it.
Kind Regards,
Chetan
Thanks for your quick reply and suggestions. I will work on it.
Kind Regards,
Chetan
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