Re: psfgen non-bonded atom pairs

From: Shirley Hui (
Date: Sat May 22 2004 - 12:35:52 CDT

I read up on the available documentation and now I think that in the section called NNB in the psf file, that these contain the non bonded pairs
This web page has an example of what I am talking about:
My question now is why when I run psfgen on my psb files, that section contains all zeros??
It's as if there are no non bonded pairs, but I don't think this is right. The molecule I am testing with is 1UBQ.pdb (ubiquitin).
Thanks for any insight,
  ----- Original Message -----
  From: Shirley Hui
  Sent: Saturday, May 22, 2004 2:08 AM
  Subject: psfgen non-bonded atom pairs

  Does anyone know if psfgen is able to given a pdb file calculate which pairs of atoms are "non-bonded" (outside a certain cutoff distance).
  For example, the psf file that is generated has a section that contains bonded atom pair which is useful when calculating bond stretch energy etc. For calculating van der waals the non-bonded pairs would be required for that calculation and I just wonder if psfgen is capable of performing the task of finding which are considered "non-bonded" given the pdb file.
  I don't believe this is possible based on the documentation that i have read, but I thought i would confirm it.
  thank you,

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