AMBER: for mask in rms

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

Here is my measure_rmsd.trajin:

trajin equil_2.crd
trajin equil_3.crd
trajin gc.md.x
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.

wy


      
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Received on Wed Jul 30 2008 - 06:07:50 PDT