From: Shirley Li (li19104_at_yahoo.com)
Date: Thu Oct 06 2005 - 16:01:42 CDT
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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