others may have more experience here but I can make a few comments:
1) in VMD, make sure you are loading the prmtop first if you want to see
bonds contained in it - don't load a pdb since it will use distances to
determine bonds.
2) capping is reasonable, though depending on your resources you could also
include part or all of the cysteine in the charge derivation. At minimum I
would suggest that the cap match the atoms to which the substructure is
bound in your final system (ie don't cap with H if you have a C or S there
during MD).
3) whether you want to use gaff or do a more complete scan depends on your
resources, and how much accuracy you need in this region during the
simulations. It's the same for any ligand - you can use gaff, but if you
want to really study a particular molecule in detail it can be worth
deriving custom parameters. both are reasonable depending on what your
project needs.
On Tue, Sep 23, 2025 at 2:03 AM js jeon via AMBER <amber.ambermd.org> wrote:
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 23 2025 - 07:00:02 PDT
