Why does eHiTS give me an error when it tries to convert the PDB file?
If you used some molecular visualization software to save the PDB file… The Protein Data Bank has a very strict file format definition for PDB files: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html. Unfortunately, most PDB files that are publicly available DO NOT follow the written standard of the format. In fact, several commercially available molecular visualization software DO NOT adhere to these PDB file conventions. Software such as Quanta do not include the “CONECT” keyword when it saves the PDB which is in fact essential to determining the correct connectivity of the atoms. These softwares use simple distance based criteria from the coordinates to GUESS the connectivity of the atoms. However, eHiTS requires the “CONECT” keyword to ensure the accuracy and integrity of the molecule. So the take home message is: if you use some molecular visualization software to manipulate the PDB file, DO NOT save it as a .pdb but instead save it in one of the other formats
