[AMBER] Abasic Site and Errant OH Group on Sugar

From: Robert Molt <rwmolt07.gmail.com>
Date: Mon, 4 May 2020 08:40:40 -0400

Good evening,

I am observing a problem of added atoms I do not desire after leap processing; I am hoping for assistance in tracking down the mistake I am making which results in these extra atoms.

Consider a protein/DNA complex given in the attached file 5.pdb. It has standard residues, but for the "ABB residue." Dr. Bergonzo kindly offered me a library file with parameters for an ABB “residue” (I re-post her file here as ABB.off). I loaded the initial pdb structure, with the leap commands specified below (I have also attached the leap.log file). I had no particular errors within leap (beyond what I believe are “innocent” warnings in the leap.log). I then proceeded to minimize and heat the system, and finally observed a problem: leap added a OH in the C1 position of the ABB residue. This was not intended. The file “stripped.pdb” shows the system post-heating (post-leap, moreover).

I believe the leap log clarifies the point of departure:

"Joining DC - ABB
  Added missing heavy atom: .R<ABB 329>.A<O1B 13>
Joining ABB - DC"


1.) I believe that this line from the leap log shows the adding the OH group I do not wish. Can this interpretation be confirmed?

2.) This would imply to me that my ABB.off file is expecting a OH residue on the C1 atom. When I examine the .off file, I see an O1B specified in the line

 "O1B" "OH" 0 1 131072 13 8 -0.648200

Is this interpretation correct? I have been trying to find the part of the AMBER manual which clarifies this file format, but am coming up short. I would think that this could be found in chapter 15, beginning page 225 of the 19th edition, but I do not see anything clarifying the .off file format. I also cannot find anything in the manual when I search for .off

3.) I am very confused how the attached .off file would result in an O1B being added to a C1’ carbon. Perhaps this answer will be forthcoming in better understanding the file format of .off files.

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Received on Mon May 04 2020 - 06:00:04 PDT
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