Hi Noureen,
In this tutorial, pdb4amber uses program “reduce” via the “--reduce” flag to add the hydrogens, including determining the optimal tautomers for histidine.
“reduce” can be used as a standalone program. You can find more information about “reduce” from the program’s site:
http://kinemage.biochem.duke.edu/software/reduce/
https://github.com/rlabduke/reduce
Or from a recent Amber manual.
In pdb4amber, the use of reduce is similar to running the standalone reduce with -build and -nuclear. The “-build” option adds hydrogens to sidechains, determine whether to flip and evaluates the histidine tautomers. The “-nuclear” option controls X-H bond lengths and might have some minor effects on the outcomes (tautomeric states).
Hope this helps!
A
From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Monday, May 6, 2024 at 3:36 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Does pdb4amber take care of protonation states?
Hello everyone,
I am following the Amber tutorial: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue. In Step 1: Preparing PDB file, there is no mention of H++ or PROPKA for assigning protonation states. Step 1 only includes using pdb4amber to "massage" the PDB file to prepare it for use in tleap. The input pdb file (1EMA.pdb) and output file (gfp.pdb) from pdb4amber in the tutorial are both attached here. In the output file, the HIS residues have been changed to either HID or HIE. Does that mean pdb4amber took care of the protonation states? Or how were those changed in the output pdb file?
Thanks,
Noureen
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Received on Mon May 06 2024 - 19:00:02 PDT
