AMBER Archive (2007)

Subject: Re: AMBER: coordinates ******

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jan 23 2007 - 15:20:10 CST

> 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.

Bill

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu