AMBER Archive (2008)

Subject: AMBER: mask for oligosaccharide

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Wed Jul 30 2008 - 13:23:58 CDT

 
Ask again, sorry.

Here is my measure_rmsd.trajin:

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

wy

      
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