AMBER Archive (2002)

Subject: Re: more about averaging

From: Bill Ross (photoriot_at_yahoo.com)
Date: Fri Nov 08 2002 - 15:21:39 CST

> The results of averaging in ptraj and carnal are
> very different for the same trajectory.

Assuming you are fitting the coordinates before
averaging (use an RMS FIT version of the STREAM
in carnal), the only difference between ptraj and
carnal is that carnal does mass-weighted fitting
by default, and ptraj does an unweighted fit.

> While in carnal I obtain a structure that looks
> very strange

This could happen if you do not fit first, also
if residues were translated across the box boundary
into the other side of the cell and not imaged back,
or if they were inherently so mobile relative to
each other that averaging is useless. (An example
of the latter is water - the molecules will normally
interpenetrate on averaging.)

Finally, if carnal & the viz program disagree on
the presence of box coords, dynamics will look
trashed; shouldn't be a problem for a single
snapshot tho.

> in ptraj I obtain a "good looking structure".
> ... Now if I look closer to the average
> structure from ptraj is identical to the initial
> structure. How can it be??

Sounds like a problem in specifying ptraj commands,
but I haven't used the program much.

Bill Ross