Or if you have any suggestions ... I tried using vienna 2.0, pyTM plug in for pymol but I do not see the change in charges when I analyze the electrostatics. ideas? Thank you in advance.
Hi Andi S. Silva hope you are doing well,
you can simply open your structure on pymol and go to the builder option and edit your particular residue, or you can open your .pdb structure in a text file and edit the same.
best wishes
Hi,
For phosphorylating the serine residues, Vienna PTM 2.0 works really good. I have used it many times, it introduces 2 negative charges (As this parameter will be chosen by you in their web server). Probably the tool you have used to analyze the charge of the modified protein does not detect the phosphorylated serine from PDB format (Because Vienna PTM changes serine code from SER to S2P in the pdb file).
If you still want to ensure this, you can download the forcefield provided by Vienna PTM 2.0, estimate the charge of the protein before and after the phosphorylation in gromacs (Follow lysozyme in water tutorial). It will clearly show you the introduction of two negative charges upon phosphorylation of your protein.
CHARMM-GUI is working perfectly for such things ;)
https://www.charmm-gui.org/
You can use Maestro to edit your PDB, it phosphorylates the residues with energy minimization.