VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon May 17 2021 - 14:23:20 CDT

Hi Harper,

Is the bond defined twice? When using patches, only *new* bonds should be defined, that don’t exist in the parent residues. If the bond is defined twice, automatic angle generation can make nonsense angles between only two atoms.

The way that angle and dihedral generation normally works is based off a bondlist that automatically generates an angle term for each pair of bonds that share a central atom. Similarly, a dihedral would be assigned for every pair of bonds that are connected themselves by a single bonded interaction. But if there are two bonds that connect the same two atoms, you’ll get duplicate angles, including some weird ones like those you are describing.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "Smith, Harper E." <smith.12510_at_buckeyemail.osu.edu>
Date: Monday, May 17, 2021 at 2:06 PM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Angles generated by AutoPSF?

Hi all,

How are angles decided by AutoPSF? I tried to make a patch for my residue, but when I apply it in AutoPSF, I have several strange angles listed in the .psf file (like 13 16 13). These should not exist, right?

Best,
Harper Smith