AMBER Archive (2004)

Subject: Re: AMBER: RMSD calculations in ptraj and Carnal

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Tue Jun 15 2004 - 15:06:38 CDT


By default, ptraj RMS fits *without* mass weighting. To do mass
weighting, simply add the "mass" keyword. Back a long time ago when testing, carnal
and ptraj give equivalent RMSd results (~1995) and the routines have not
changed significantly since then.

  rms first mass out rms.dat @CA

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