normal lipidated amino acids in martini3

  • poojaric
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11 months 4 weeks 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

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11 months 4 weeks 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

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11 months 3 weeks 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

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