AMBER Archive (2009)

Subject: [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Jul 08 2009 - 04:45:41 CDT

Dear Sir/Madam,

 

I tried to study the effect of mutation for a protein. I tried several starting geometries and protocols. I also found the rmsd of wild type protein (~3 A) larger than that of mutant one (~2A), compare to the starting geometry after the minization (before md starts). Is this difference acceptable? I plot the rms over time for the two systems, I found the rmsd of the wild type is consistently higher than that of mutant one. But should I comment on the difference between 3 A vs. 2 A? Is the different too small to be sound biologically?

 

Does 3A rms acceptable in general?

 

How can I confirm if the differences in rms is because of my mistakes or the real biological differences of the two proteins?

 

Bst regards,

CAt

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