I want to perform an MD simulation for the phosphorylated protein. But whenever I add phospho-group to the structure using Pymol tool, the MD simulation is not executed at all because it repeatedly shows there are unwanted residues like "PTR" or presence of P in the residue(Or phosphate in the residue). How to solve this problem ?
You need to add the parameter/topology files for the modified residue to your MD program.
You can use charmm-gui to prepare your system... They have parameters for pretty much all phosphorylated aminoacids
as Mario E. Valdés-Tresanco said, You can use Charmm-gui to modify your residues whilst preparing your system.
It should be noted that your phosphorylated residues are non-standard residues, which means that not all of their parameters are included in the forcefield.
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