In my MD running, by using the amber99SB force field, but there is a non-standard residue, phosphorylated Aspartate, no parameters for this residue. How do I generate parameters for this residue?
The integrity of a force field depends on the fact that parameters have to be developed in a compatible way. The AMBER force fields are well documented in the literature, so the short answer is: read the relevant paper(s) and do the same thing. Likely QM optimizations and charge calculations will be necessary.
Thank you for your information. I already construct a library for this residue by using the
Antechamber with GAFF forcefield, but I am not sure whether in Gromacs I can use two force fields, amber99SB for the protein, but GAFF for this modified residue, Do you have some experience about this?
This builder supports couple of force fields.
http://compbio.biosci.uq.edu.au/atb/
Also you can follow the philosophy of your selected force field to derive what ever parameters you need.
- Badges
- Science topic