Hi,
I need help with performing a simulation of a ligand and a protein.
I am using psfgen code and add a ligand as the second segment but my parameter file couldnt recognize the new molecule (known chemical).
I wonder how should I add it to parameter file?
Thank you very much
Regards
Farzaneh
Hi Farzane,
Well, by default force fields for biomolecules only include parameters for proteins or lipids or nucleic acids. You need to find a way to parametrize your non protein ligand. Have you parametrized your ligand?
Assuming you have not:
If you have access to gaussian software you might want to do that using Force Field Toolkit of VMD. If not then check out CGenFF (Charmm General Force Field). (Beware that this is a less accurate approach). Alternatively you could search in ligandbook (https://ligandbook.org) to see whether somebody else already parametrized your ligand before (parameters might not be compatible with CHARMM though).
Hi Farzane,
Well, by default force fields for biomolecules only include parameters for proteins or lipids or nucleic acids. You need to find a way to parametrize your non protein ligand. Have you parametrized your ligand?
Assuming you have not:
If you have access to gaussian software you might want to do that using Force Field Toolkit of VMD. If not then check out CGenFF (Charmm General Force Field). (Beware that this is a less accurate approach). Alternatively you could search in ligandbook (https://ligandbook.org) to see whether somebody else already parametrized your ligand before (parameters might not be compatible with CHARMM though).
Dear Onur,
Thank you very much for the informative and detailed answer.
Bests
Dear Farzane,
You can search in zinc database for mol2 file of your ligand and then upload it here and get your parameters file
https://cgenff.paramchem.org/initguess/
Thank you very much Mohamed, I checked step by step. Hence, after merging the PSF and PDBs I can do the simulation( I wonder which software or server is better! the first thing comes to my mind is merge structure of VMD).
second question is they asked for a mol2 file contains all hydrogens. what should I do in the case I have some missing?
I am also using VMD and I have not tried another software yet. Regarding the hydrogen , since mine were not missing I did not face a problem but I would like to know exactly like you ... hope can someone add answer here for that ...
Best
- Badges
- Science topic
- Similar topics
- Filing