AMBER: mask for oligosaccharide

From: Wenyong Tong <>
Date: Wed, 30 Jul 2008 11:23:58 -0700 (PDT)

Ask again, sorry.

Here is my measure_rmsd.trajin:

trajin equil_2.crd
trajin equil_3.crd
reference gc_annMD_min_2.rst (from NMR refinement)
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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Received on Sun Aug 03 2008 - 06:07:15 PDT
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