AMBER Archive (2006)

Subject: Re: AMBER: RMSd error

From: Thomas Cheatham (
Date: Fri May 26 2006 - 10:59:34 CDT

> > I am still trying to figure out why I do not produce PMSd data for the
> > entire trajectory that I am reading in ptraj. I am enclosing the
> > output file from ptraj below. I still cannot identify any errors. It
> > seems that all sets were read in, and that the output file was
> > generated correctly. Just I get RMSd valvues for 719ps out or a total
> > of 1820ps I simulated. Can anyone pick up what I am missing please?
> > PTRAJ: rms first out
> > /DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms @CA time 0.2

Here you are saying each frame represents 0.2 ps of time...

> > PTRAJ: Successfully read in 3598 sets and processed 3598 sets.

You read in 3598 frames; the first trajectory contains only 398 frames.

> > PTRAJ RMS: dumping RMSd vs time data

You should get a RMSd data file that contains 3598 lines of text (one
value per each frame) which can be checked via "wc -l *.rms"

Let me know if there is still a problem you do not understand.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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