autoionize and psfgen, which one first?

From: Shirley Li (
Date: Thu Oct 06 2005 - 16:01:42 CDT

Dear NAMDers,

I have a protein .pdb file. In order to run MD, I
need to generate .psf file (with psfgen) and add ions
(with autoionize) to neutral the system. My question
is: which one I should run first, PSFGEN or
AUTOIONIZE? I notice that the latter requires .psf
file, while the former requires the .pdb file for the
ions if I want the .psf for them as well.

Thanks a lot for your help in advance.


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