AMBER Archive (2008)

Subject: AMBER: for mask in rms

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Tue Jul 29 2008 - 22:35:23 CDT


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

      
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu