Re: AMBER: coordinates ******

From: Bill Ross <>
Date: Tue, 23 Jan 2007 13:20:10 -0800 (PST)

> Some of the coordinates are missing and instead a line
> of asterisks appears.

It may be easiest to rerun your calcs with a more gradual equilibration.

> These lines are problematic whenever I try to run
> ptraj and carnal. The programs exit when they reach
> those lines and print an error message in the logfile.

> 2) Do you think that removing solvent molecules might help?

If only solvent molecules generate the "****" fields, yes. You
would have to write a program to strip them since carnal and
ptraj won't.

> 3) If I do not center the structures after removing
> solvent molecules, do you believe it is still possible
> to perform trustworthy diffusion analysis

Not sure.. you can align using rms fit in case that helps.


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Received on Wed Jan 24 2007 - 06:07:43 PST
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