On Mon, May 06, 2024, Abdelrahman, Noureen via AMBER wrote:
>
>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?
Several points:
1. If you use the --reduce option in pdb4amber, reduce will add hydrogens,
but not explicitly based on any pKa calculations.
2. If the input pdb file has hydrogens, pdb4amber will figure out which
protonation state each HIS residue has, and change the residue names
appropriately.
3. Starting with AmberTools24, we are including pdb2pqr (which calls propka3
internally) to assign protonation states. See Section 12.6 of the Amber
2024 Reference Manual for more information.
...hope this helps....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 06 2024 - 20:30:02 PDT
