GROMACS version:2018
GROMACS modification: No
I performed a MD simulation on a protein-ligand complex using AMBER99SB force field and my protein contains zn between 4 CYS. after I Perform em step and looked at the em.gro, zn has changed it place and was not inside the protein any more. What do you propose me to do?
Do you have any information about the protonation of you Cys sidechains?
one or more of them might be deprotonated, which would make a large
difference for the stability of the resulting Zn complex… if you don’t have exptl. values try to
figure out the pKA of these residues using tools like propka or H++
Thank you @michael.brunsteiner for your reply.
All of my cys side chains are protonated.
I had read something about distance restrain using harmonic potential (bond func. type 6) and seems its working. But I don’t know how to use that.
Can anybody help me with this ?
information about any additional constraints should be given in the topology file. the gromacs documentation gives clear instructions on how to do that - so i recommend reading the documentation.
However, before using constraints I’d try to make sure that the Cys thiol groups are really all protonated. Given the intrinsic pKA of this group, and if its sitting right next to a Zn2+ ion, chances are its actually de-protonated … you write: “all of my cys side chains are protonated” … how do you know that? If you infer this simply from what’s in your structure file (pdb) you should double-check where this structure comes from, and how it was protonated. As for tructures from x-ray experiments - if they have positions for H atoms - these are usually not an experimental result, but a MODEL … which might be accurate or not … figuring out the exact protonation of a protein can be highly non-trivial, and most commonly used models are not very accurate.
You have a zinc metal center. You can build your model using Antechamber with ZAFF.