Dear Amber Users and Developers,
I have prepared a simulation for a protein-ligand complex with a covalent
bond to a cysteine residue, and I would be very grateful for your expert
review of my setup protocol.
My overall strategy was based on advice from a 2021 mailing list post by *David
A. Case* (archive.ambermd.org/202107/0152.html), where the modified
cysteine (CYX) and the ligand are treated as separate residues joined by a
bond command in tleap.
My workflow is:
1.
*PDB Prep:* Edited the PDB to rename the reactive Cys to CYX and cleaned
the file with pdb4amber.
2.
*Ligand Params:* Used the "cap-trick" method (adding and removing a
temporary H atom) to derive stable AM1-BCC charges for the final ligand.
Generated LIG_final.frcmod with parmchk2.
3.
*Cross-link Params:* Manually created frcmod_link_sg.frcmod by adapting
analogous parameters (e.g., ss-c3, X-ss-c3-X) from gaff2.dat to define
the bond, angle, and dihedral terms at the S-c3 junction.
4.
*tleap Assembly:* Loaded both frcmod files, used the bond command to
create the link, solvated, and added ions. The process completed without
errors.
I have confirmed that the covalent bond is correctly listed in the topology
file using the printBonds command in ParmEd. (Also, is it expected behavior
in VMD not to visually render the S-C bond that was created with the bond
command in tleap? I have confirmed the bond exists using ParmEd, but it
doesn't appear visually by default.)
Based on this, I have two specific questions:
1.
Is this overall workflow—specifically, using the "cap-trick" for ligand
charges and manually creating a linking frcmod file from analogous GAFF2
parameters—a correct and physically sound method for setting up this type
of covalent system?
2.
Is this manual parameterization generally considered sufficient, or is
it highly recommended to perform a more rigorous refinement (e.g., a PES
scan and fitting with *paramfit* or *mdgx*), especially for the dihedral
terms around the new covalent bond?
Thank you for your time and guidance.
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Received on Mon Sep 22 2025 - 23:30:02 PDT
