Re: [AMBER] Serious problem at specific time point

From: Thomas Cheatham III <>
Date: Wed, 10 Nov 2010 17:09:37 -0700 (Mountain Standard Time)

> When I calculated RMSd of catalytic domain of enzyme, slope was suddenly
> soared at 4.8ns (I attached a plotting data). So I ran the VMD to visualize
> what happened at this point, as I attached, protein structure was suddenly
> collapsed at that point !
> This is my second try. This problem was occurred at almost same point when I

Let me guess: ascii trajectory, > 2 GB, trajectory was imaged/rms fit with
ptraj from AmberTools prior to viewing it? This is a bug that plagued me
until yesterday; fixed by Dan Roe and it is working it's way through the
bugzilla chain and hopefully soon to the bugfix page...

To get around this for now, use an earlier version of ptraj (amber10) or
get the older standalone version from:


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Received on Wed Nov 10 2010 - 16:30:02 PST
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