AMBER Archive (2008)

Subject: AMBER: for mask in rms

From: Wenyong Tong (
Date: Tue Jul 29 2008 - 22:35:23 CDT

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.


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