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protonate for amino acid
- yuhui234
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13 years 2 months ago #522
by yuhui234
protonate for amino acid was created by yuhui234
how to protonate for amino acid for arg and lys in cg simulation using martini parameter?
Thanks!
Thanks!
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- xavier
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13 years 2 months ago #528
by xavier
Your question is not clear! ARG and LYS are protonated by default in most force fields as this is their protonation state at physiological pH.
If your question is about how to use "deprotonated" ARG and LYS, then you have to generate your topology as if they were protonated (charged) and edit the topology to modify the ARG/LYS that you want to be deprotonated (uncharged). You have to modify the residue name (ARG->ARG0 or LYS->LYS0, check the martini_v2.1_aminiacids.itp for details), atom type and the charge in the "[ atoms ]" section of your topology. You should replace the ARG/LYS atom definitions by the ones of ARG0/LYS0 that you'll find in the file martini_v2.1_aminiacids.itp. The bonded terms are identical so that you do not have to modify them.
XAvier.
Replied by xavier on topic protonate for amino acid
yuhui234 wrote: how to protonate for amino acid for arg and lys in cg simulation using martini parameter?
Thanks!
Your question is not clear! ARG and LYS are protonated by default in most force fields as this is their protonation state at physiological pH.
If your question is about how to use "deprotonated" ARG and LYS, then you have to generate your topology as if they were protonated (charged) and edit the topology to modify the ARG/LYS that you want to be deprotonated (uncharged). You have to modify the residue name (ARG->ARG0 or LYS->LYS0, check the martini_v2.1_aminiacids.itp for details), atom type and the charge in the "[ atoms ]" section of your topology. You should replace the ARG/LYS atom definitions by the ones of ARG0/LYS0 that you'll find in the file martini_v2.1_aminiacids.itp. The bonded terms are identical so that you do not have to modify them.
XAvier.
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