Is there a general way to do this? Can I just take the values of similar atoms from the force field I want to use for the protein? (Btw, is there a suggested one that works better for proteins?)
Please help :)
Jobin Thomas
https://manual.gromacs.org/2021/user-guide/force-fields.html
You can refer the tutorial page of Gromacs (nicely explained)
Regards
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Joel Subach
Hi if you want parameters for your molecule try ffTK, if so feel free to ask me further, happy to help:)
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Arpit Jain
Use existing force fields (e.g., CHARMM, OPLS) for atoms similar to your molecule. Generate topology using Antechamber or ACPYPE for small molecules. Use GROMACS tools like pdb2gmx for proteins, or manually adjust parameters if necessary. Recommended protein force field: CHARMM or AMBER are widely used.
To generate a force field for a molecule in GROMACS:
Adjust parameters if your molecule differs significantly from existing ones.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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