I was trying to use antechamber to obtain the mol2 file for a silicon containing molecule. But GAFF2 force field does not have the parameters for silicon and that's why antechamber could not recognize the 'si' atom. Can anyone kindly help me regarding this issue?
Hi Gourav,
As my knowledge domain does not include the parameter of a silicon force field, there are a few approaches you can consider:
1. You can use any available silicon force field parameter that has been published in the literature.
2. If your molecule is small, you can utilize servers such as ATB, Ligpargen, Charmm-gui, SwissParam, or CGenFF, which provide software-specific force field parameters. If you obtain Charmm force field parameters, you can convert them to AMBER or Gromacs formats.
3. You can parameterize the force field yourself by performing QM and frequency calculations and extracting specific force constants. A helpful resource for this approach is "Calculation of Intramolecular Force Fields from Second-Derivative Tensors."
Best regards,
Aashish
Thank you, Aashish Bhatt. But how can I convert CHARMM force field parameters to AMBER format?
There are multiple ways to convert parameters in molecular simulations, and two popular methods are using CHARMM-GUI and ParmEd.
1. You can use Charmm-GUI for froce field converter.
https://www.charmm-gui.org/?doc=input/converter.ffconverter
2. Parmed
https://parmed.github.io/ParmEd/html/readwrite.html
Another option for parameter conversion is ACPYPE, which is a Python script that automates the conversion of Amber typologies and parameters to GROMACS or CHARMM format.
https://github.com/alanwilter/acpype
Thanks,
Aashish
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