Made by Supernova (https://www.zhihu.com/people/zhang-jia-xing-42-34)
Because of the difference atom name rules between DS and Gromacs, the pdb file generated by DS's Prepare Protein protocol cannot be directly passed into Gromacs.
Herein, I wrote a simple program, to convert the protein prepared by DS into the format that gromacs can identify.
- Rename His to HID, HIE and HIP according to H type
- Rename Asp to ASP, ASH according to whether contains HD2
- Rename Glu to GLU, GLH according to whether contains HE2
- Rename terminal O from OCT[12] to OC[12]
- Usage 0: pdb_cleaner # directly show this help message
- Usage 1: pdb_cleaner input.pdb output.pdb
- Usage 2: pdb_cleaner input.pdb # default output to new.pdb
# get test.pdb file prepared by DS
pdb_cleaner test.pdb # generates new.pdb
gmx pdb2gmx -f new.pdb