Hi All, I have a PDB file and want to convert the PDB to MOL2 format. The PDB has missing residues which is not a problem but when I write to MOL2 format it assigns the pseudobond and I really no need of it. I tried to solve it by checking the thread but I am not getting a clear solution for my problem. Last, I am doing this by using the script as I have >1000 PDBs to process the same way so the command line would be preferred. PS: I send you the molecule in PDB format as an example case. Thanks in advance, Kiruba ________________________________ This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message.