eRMSD on modified nucleotides

[Mandar Kulkarni]

Hello,

I am working on RNA simulations with modified nucleotides (modified bases) (for e.g. pseudouridine). 

Given C2, C6, C4 atoms are present is modified bases, can eRMSD work correctly? 

Or it would be better to explicitly define atoms with "lcs" kind of group for eRMSD biasing?

Thanks in advance,

Mandar

[Giovanni Bussi]

I would suggest defining them by hand. In any case, if you select them using plumed lcs, you should be able to see the selection in the log file and verify if it's correct

Giovanni

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[Mandar Kulkarni]

Thanks for the reply. I guess I have to follow a separate atom order to describe purines and pyrimidines.

• C2,C4,C6 for pyrimidines
• C2,C6,C4 for purines

Best Regards,

Mandar Kulkarni

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[Mandar Kulkarni]

Is it possible to choose different base atoms other than C2, C4, and C6?

Best Regards,

Mandar Kulkarni