While doing autodock for my moleucle which contains a bromine atom, after completing the docking process, while i am analysing the output poses, always the bromine atom is out of the moleule with out forming any bond, please suggest how to solve this problem.
It may be an artifact of visualization (cutoff distance for linking atoms). What is the carbon-bromine distance in the docking pose?
"A survey of 60 bond distances between monovalent bromine atoms and carbon atoms in aromatic rings has been carried out. The new expectation value for the Br-C linkage is 1.8966 A with an associated standard deviation of 0.0019 A."
Article On the bond distance between bromine and aromatic carbon atoms
Martin Klvana , thanks for your answer, the C-Br distance in our molecule is about 1.88 Angstroms
Probably the connectivity information got lost during export or file type conversion. You can explicitly define the connectivity information in the PDBQT or PDB files. These files are text files; you can open them in any text editor (avoid Notepad, try gedit or vscode) and modify the records or append new information. Here's how to define CONECT information in a PDB file:
https://www.wwpdb.org/documentation/file-format-content/format33/sect10.html
Uttam Pal , thanks for your answer, as i check the connectivity information, it is still there with out any errors, when i open the file in pymol, the bond is in connected state but when i transfer the file to the discovery studio (biovia) viwer , the above stated probelm is appearing
Satyanarayana Swamy Vyshnava -- can you share the PDB file of the ligand?
Martin Klvana , here i shared the file for your reference
See the attached file, Use the attached file if required, (add required hydrogen atoms)-if it is correct.
Nikhil Maroli thanks, i will check and let you know back
Use AutoDockTools to convert your output files to pdb, maybe that won't solve your problem but it's a good practice. Whereas the software was created by the same group.
Hi Satyanarayana Sv, I am also facing the same problem as yours. Have you solved your problem? If yes, then please suggest me also the way you have done.
Try to save the file under Grid/Macromolecule/Choose tab if it is a protein
So, After reading the file out( pdbqt) of docking by discoverystudio ; Scripts then structure editing - Group union and clik atom Brom and other group to link them
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