Hello, all!
I am very new to constant pH molecular dynamics, but I have read through
the tutorials on the AMBER website (8.1 and 8.2). However, they have all
utilized standard amino acids with predefined titration info. As such, I am
largely confused as to how to define nonstandard titratable residues in
$AMBERHOME/AmberTools/src/parmed/parmed/amber/titratable_residues.py. I
have read the example CYS definition in Section 24.5 in the AMBER20 manual
(page 517), but am wholly confused as to what was actually done to set that
definition.
For context, I intend to simulate a dibasic molecule with two pH-sensitive
amine groups in the IGB8 implicit solvent model. My general plan is to:
- draw each protonation state (+2, +1, and 0) in xLEaP and save them as
PDB files.
- utilize the gaff2 force field to perform partial charge derivations
for each protonation state in antechamber
- calculate reference energies between all three protonation states (+2
vs. +1, +1 vs. 0, +2 vs. 0) via thermodynamic integration
- use those reference energies to define my dibasic molecule in
titratable_residues.py, along with experimental pKa1 and pKa2 values.
I want to make sure that I understand this process before I proceed. Are
there any tutorials that I can reference so I can understand the CYS
definition better? Furthermore, would it be possible to define a titratable
residue with two pKas in titratable_residues.py?
Any advice that you can provide would be much appreciated!!!
*All the best,*
*Nathan D. Black*
*Texas A&M University - Corpus Christi*
*Instructor of Chemistry*
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Received on Tue Oct 10 2023 - 15:30:02 PDT
