I want to simulate a protein using PDB file extracted from Protein Data Bank. After inspection, I noted that the protein atoms in the PDB has ANISOU atoms. In my understanding, this type of atoms has two coordinates as they are flexible (correct me if I am wrong).
My question is, can I run a molecular dynamics on this PDB file? Do I need to do any pretreatment?
Dear Mr Bhavaniprasad, thanks for your quick reply.
The anisou lines have been discarded successfully. Again, thanks! :)
You can do many protein modification, follow my answer in here:
https://www.researchgate.net/post/How_do_I_remove_Anisou_from_a_PDB_text_file_in_UBUNTU_by_command
This is my suggestion:
As an alternative, you can also use PDBest, it's multi platform. Its website: http://www.pdbest.dcc.ufmg.br/ It provides many features and can process many PDB files for the same treatment. Of course, one of them is to remove ANISOU.
- Badges
- Science topic