AMBER Archive (2006)

Subject: Re: [UCE]AMBER: RE: trouble stripping waters with ptraj

From: Thomas Cheatham (
Date: Tue May 30 2006 - 12:17:31 CDT

> Thank you very much for your reply. I have one question about your suggestions. You wrote:
> Check out the produced RMSd files to see if this makes sense. You could
> also create an average structure,
> average avg.pdb pdb
> and look at this...
> I looked at the produced RMSd files and they seem fine, but I'm not sure
> what you mean when you suggest that I create an average structure. What
> trajectory would I be averaging, and what would I be looking for in
> order to confirm the validity of the RMSd files that were produced? If
> you could please clarify what you meant, I would be very grateful.

If there is something wrong with a mismatch between the prmtop and
trajectory, or corruption of the trajectory, or some other artifact, this
can be easily viewed by looking at an average structure created from the
trajectory. In the script that calculated the rmsd values, you could add
a line as above (average avg.pdb pdb) after the rms command...

In general, judging the reliability or validity of the data produced from
MD simulation is up to you. You can monitor the potential energy,
temperature, pressure/volume/density, and other indicators of reliability.
If, for example, the RMSd plot shows rapid spikes (usually indicative of
imaging issues where one of the molecules is imaged back into the box if
you have multiple molecules) or continuously rises (suggesting the
molecule may be unstable), you can look at a movie of the trajectory to
see if the behavior is consistent or expected or reasonable. The average
structure is another easy way to see if there are problems as if there are
"problems", the produced average structure often looks nothing like what
you expect; another possibility is using the MM-PBSA analysis on the

I think that if your RMSd plot looks reasonable, the stripping of water
worked as expected. If you want to verify further, look at a movie of the
trajectory and/or the average structure. See the AMBER tutorials at for more guidance (such as the DNA
tutorial among others).


\-/ 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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