Re: AMBER: TMD and "Current RMSD from reference"

From: Thomas Cheatham III <>
Date: Sun, 23 Sep 2007 12:30:31 -0600 (Mountain Daylight Time)

> Is it possible to reproduce the sander output's targetted rmsd results
> ever using ptraj? I do not think so. Here is a test case I have done.
> reference xraymin.rst
> trajin tgtmd_1.traj
> rms reference out rms_out_testing :1-18

Try adding the "mass" keyword; the RMSd in the targetted MD is mass

rms reference mass out rms_out_testing :1-18

-- tec3
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Received on Mon Sep 24 2007 - 17:45:09 PDT
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