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