Protein mutations

[velocirraptor23]

Hi,

I have checked protein mutation implementations, including charge residues and proline transformations. Is this something we can use in somd2 straight away? If so, is repex also available for it?

Many thanks,

Cesar

[akalpokas]

Hi, yes cases are usable in SOMD2 and have been tested. You can use repex for both as its a separate additive feature of SOMD2 which does not depend on the use case, rather it affects the dynamics ran by SOMD2 instead.

[velocirraptor23]

Hi,
Thanks for your reply.
How long do you recommend running these transformations? I assume repex can help them to converge faster.

[akalpokas]

Sorry for the delay in replying. If it's a mutation that doesn't cause a structural rearrangement, 5-10ns per λ-window should be fine. If it does then much longer sampling is needed. dG convergence & 2D RMSD plots are good diagnostic tools here to check for potential sampling problems. Repex will help things quite a bit yes.