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lipidated amino acids
- poojaric
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4 years 9 months ago #8195
by poojaric
lipidated amino acids was created by poojaric
Dear All,
I would like to simulate lipidated protein.
I came across this paper pubs.acs.org/doi/10.1021/acs.jpcb.7b10175 where they have parameters for lipidated amino acids for use with Martini
force field. I went to their github page to download the files but I could not find the
martinize.py script which includes parameters for lipidation.
Please can someone suggest me how do I use their files to lipidated certain residues on my protein.
Looking forward to your replies.
Kind Regards,
Chetan
I would like to simulate lipidated protein.
I came across this paper pubs.acs.org/doi/10.1021/acs.jpcb.7b10175 where they have parameters for lipidated amino acids for use with Martini
force field. I went to their github page to download the files but I could not find the
martinize.py script which includes parameters for lipidation.
Please can someone suggest me how do I use their files to lipidated certain residues on my protein.
Looking forward to your replies.
Kind Regards,
Chetan
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- riccardo
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4 years 8 months ago #8202
by riccardo
Replied by riccardo on topic lipidated amino acids
Did you try the version of Martinize which is linked here:
www.cgmartini.nl/index.php/430-lipidated-aminoacids
(namely:
github.com/raziel81/Martinize/tree/razie...pidated-aa/martinize
)?
*Note* that it is a different version from the latest Martinize version (which you can instead obtain from here: cgmartini.nl/index.php/tools2/proteins-a...layers/204-martinize ).
*Note* that it is a different version from the latest Martinize version (which you can instead obtain from here: cgmartini.nl/index.php/tools2/proteins-a...layers/204-martinize ).
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- poojaric
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4 years 8 months ago #8206
by poojaric
Replied by poojaric on topic lipidated amino acids
Hi,
I got the modified martinize.py from the authors. Its working fine.
Kind Regards,
Chetan
I got the modified martinize.py from the authors. Its working fine.
Kind Regards,
Chetan
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- Deep684
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2 years 11 months ago #8922
by Deep684
Replied by Deep684 on topic lipidated amino acids
I am also looking for that modified martinize.py to prepare a coarse-grained lipidated protein.
Can someone please help me with file.
Thank you.
Can someone please help me with file.
Thank you.
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