AMBER: for mask in rms

From: Wenyong Tong <>
Date: Tue, 29 Jul 2008 20:35:23 -0700 (PDT)

Here is my measure_rmsd.trajin:

trajin equil_2.crd
trajin equil_3.crd
reference gc_annMD_min_2.rst
strip :WAT :Na+
rms reference out rmsd_to_NMR.dat

My question is how to define the mask for sugar (e.g. rms reference out rmsd_to_NMR.dat .C, O, H ???). If I did not define, the result is different from the one calculated from VMD.

Thanks in advance.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Jul 30 2008 - 06:07:50 PDT
Custom Search