GROMACS version: 2024.1
GROMACS modification: No
Dear all,
I would like to start a dynamic on a protein whose aspartate residue is phosphorylated. I’d like to use Charmm36, but although I’ve read that there are files for serines, I can’t find any information for asparates. How can I do this? Thank you for your help.
With kind regards,
Manon
CHARMM36 does not support phosphoaspartate. You will have to parametrize it yourself.
Dear Jalemkul,
Thank you for your reply. Would you have any advice for this parameterization? This is the first time I’ve had to do one.
The methods for parametrizing with the CHARMM force field are extensively documented in the literature, in various reviews of the force field and in the CGenFF papers. Note that parametrization is considered an expert topic; if you are unfamiliar with how to perform QM calculations, vibrational frequency analysis, energy scans, etc. you will probably want to work with someone who is.