No hard atom or residue naming conventions exists for pdb files. Applications which output pdb files will generate them for a specific target audience, disregarding formatting needs of other audiences. To overcome this problem, a simple python script has been developed which reformats pdb files to make them compatible mainly with the ADUN Amber* formats. The application is in the Adun/Scripts folder and is executed the following way:
repairpdb.py PDBFILE OPTION1 [OPTION2...]
It is able to:
- correct hydrogen namings [hyd, hyd2]
- clean the pdb file from everything that is not coordinates [clean]
- renumber the residues from 1 to x [numb]
- renumber the atoms from 1 to x [numb2]
- add capping to the terminals [cap]
- remove capping [decap]
- rename histidines according to protonation state [his]
- remove protonation state naming [dehis]
- correct cysteins with sulfide bridges [cys]
- remove sulfide bridge corrections [decyx]
- convert to ambercg coarse-grain [aa2cg]
- rename chain names to A…Z [chain]
- standardize position of atom names [atom]
- correct rna atom names [rna]
- cap protein according to enzymix [enzymix]
