From: Smith, Harper E. (
Date: Mon May 17 2021 - 14:57:28 CDT

Hi Josh and Paweł,

You are absolutely right -- I had defined a bond that already existed. Removing that bond fixes the issue. Thank you!

Harper Smith
From: <> on behalf of Pawel Kedzierski <>
Sent: Monday, May 17, 2021 3:50 PM
To: Smith, Harper E. <>; <>
Subject: Re: vmd-l: Angles generated by AutoPSF?

Dear Harper,
W dniu 17.05.2021 o 19:15, Smith, Harper E. pisze:
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?

I would suggest checking if you do not apply the same patch twice, or whether the patch does not duplicate the same bond.

With regards,


Harper Smith