From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Oct 06 2005 - 16:11:43 CDT
PSFGEN. The ions will be added both to the psf and pdb by Autoionize.
This usually will be your last step.
On Oct 6, 2005, at 4:01 PM, Shirley Li wrote:
> 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.
> Yahoo! Mail - PC Magazine Editors' Choice 2005
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