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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- application/octet-stream attachment: 1EMA.pdb
- application/octet-stream attachment: gfp.pdb
Received on Mon May 06 2024 - 13:00:02 PDT
