GROMACS version:2019-4
GROMACS modification: Yes/No
I want to perform molecular dynamics simulation of drug carrier and drug molecule.
so for that i used phosphorene sheet as drug carrier. i am beginner to this, How to parameter this sheet for Charmm36.jul2022.ff
can you guide me how to do this in gromacs.
Thanks in advance
You can generate topologies for the CHARMM forcefields using CGenFF. I’m not sure what your background with md simulations is, but a good starting place is to go over the first lysozyme-in-water tutorial if you need help with the basics, then the fifth protein-in-ligand tutorial which should be closest to what you’re looking for. Feel free to ask follow-ups if you run into any further issues!
Thank you very much Karis. yes, I tried the CGenFF server to create .str file for phosphorine, but CGenFF did not recognize the Phosphorus atom. I want to get the phosphorene topology for the CHARMM forcefield. while doing pdb2gmx I got the error as Phosphorus atom is not in the atomtype. Can you help me, how to overcome and prepare topology?
Thank you
Yeah, I just tried it on app.cgenff.com and it seems any non-phosphate, non-phosphonate phosphorus isn’t supported by CGenFF. I think this might be specific to Charmm, so could you try this with some of the other forcefield options? The fifth tutorial in the link I’d sent should have options methods to parametrize for other forcefields
If you need to convert your file to a specific format for some of them, you can use openbabel to do so
Have you tried to see if Charmm-gui works? I’m not familiar with it myself but I just saw from another post that it’s another way to get parameters
Yes, I tried Cgenff and Charmm-gui. both do not work for my Phosphorene sheet. i tried to use antechamber but I am not familiar with that software. can you give me suggestion to solve this
Regarding antechamber, using acpype (the python interface) might make things easier (here is a tutorial for using it through command lines, and here is a tutorial for using it through the python API). I’m not super familiar with it myself but I tried it out with a phosphorine molecule and it seems to work.
If that’s still not working, you could also try out LigParGen for the OPLS forcefields or ATB for the GROMOS forcefields
Thank you Karis , I doubt using acpype python interface, I should use antechamber for the Phosphore sheet before acpype python interface. in the Phosphorene sheet I have more than 100 atoms is it possible to use ligpergen or ATB to create ligand topology?.
guide me to overcome this
Were there any errors that popped up when you tried acpype, ligpargen or ATB? Unfortunately, I’m not familiar enough with the software to know for sure which molecules they would respond well to or if the size of the molecule matters, but trying them out on your file should be relatively straightforward. For ligpargen and ATB, you can submit the structure to an online server, and for acpype, once you install it, enter acpype -i ligand.pdb into the terminal as instructed in the tutorial I linked
If the size is a problem, my understanding is that the phosphorene sheet is made up of multiple repeating subunits, would you be able to get coordinate files of those subunits on their own to make topologies out of (similar to how each amino acids all have their own defined topologies which the forcefield pulls from to define the full protein)?
Ok thank you for clear explanation. From literature they use Antechamber . Then use acpype python interface to conver antechamber file into gromacs topology file .but I am not familiar with antechamber .