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Disulfide Bond in Martini Force Field
- initram
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9 years 1 month ago #4467
by initram
Disulfide Bond in Martini Force Field was created by initram
Hi,
I have one disulfide bond in my protein but I am not aware of systematic treatment of these bonds in Martini FF.
Is there a "correct" approach for disulfide bond?
Thank you very much
I have one disulfide bond in my protein but I am not aware of systematic treatment of these bonds in Martini FF.
Is there a "correct" approach for disulfide bond?
Thank you very much
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- Pim
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8 years 11 months ago #4527
by Pim
Replied by Pim on topic Disulfide Bond in Martini Force Field
If you generate your protein topology using martinize.py you can specify disulfide bonds using the flag -cys (see martinize.py help for syntax).
I think it makes a bond with d=0.39 nm and force constant = 5000 kJ/mol,
but doesn't generate angles or dihedrals.
There is no specific treatment in Elnedyn if that's what you are using for your protein, you still need the bond in your topology.
I think it makes a bond with d=0.39 nm and force constant = 5000 kJ/mol,
but doesn't generate angles or dihedrals.
There is no specific treatment in Elnedyn if that's what you are using for your protein, you still need the bond in your topology.
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