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Hello,

I'm currently I'm using the residue CYSP (palmitoylated cysteine) from toppar_all36_lipid_prot.str and have been looking at the force field. Now I was expecting to find an included CMAP term since the palmitoylation is at the side chain and CMAP deals with the backbone. But there is none. Actually there is none for any lipid-modified cysteine (CYSF, CYSG, CYSL). There also is none for myristoylated glycine (GLYM) which I can kind of understand understand because there the lipid modification is attached to the backbone. But there is a CMAP term for unmodified cysteine (obviously) and also for myristoylated lysine (LYSM) where the lipid modification is also attached to the side chain like for lipid-modified cysteine.

Now I'm confused about this. What is the reason why there is no CMAP term for CYSP but there is one for LYSM? Shouldn't it be included for higher accuracy?

Thanks,

Alexander

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rmv Offline
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It could be an oversight, since the LYSM residue in the same file does have the CMAP term added for the backbone atoms. I'll check.

Confirmed, it is an oversight. The fix is simple, just copy the CMAP line from LYSM to the CYSx residues.

Last edited by rmv; 09/03/21 08:19 PM. Reason: Confirmation

Rick Venable
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The fix noted above will be included in the next release of the CHARMM force field files, coming soon to both charmm-gui and the MacKerell Lab force field site. Thank you for reporting the issue.


Rick Venable
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Thanks for the quick info. I'll fix it in my files.

Alexander


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