i'm doing docking using pyrx software.
i synthesis my compounds and draw the structure using chemdraw and do minimization energy (MMF) using chembio3d ultra and save it as .MOL2.
i added my ligand (.MOL2) to pyrx and it will automatically convert the file into .PDBQT.
when i checked the .PDBQT file, the bonding of my structure has changed. how can i overcome this problem?
thank you...
What do you mean by bonding is changed? is it visualisation problem or the bonding parameters are changed?
i mean, the original structure is single bonded in mol2 but after converted, it becomes double bonded in pdbqt file. i attached file to make it clearer
If you are using Open Babel - it seems to be broken for the PDBQT format.
Hi all, I also faced the same problem and could not find a solution for correcting pdbqt files. Then I produced pdbqt files on Pyrx and ADT, respectively. Outputs of these two programs are the same and seems correct. Additionally, when I compared obabel pdbqt and adt pdbqt files in .txt format, I saw that there were many differences between the two. For example HETATMs were not present in pdbqt files constructed by obabel command in terminal.
On the other hand, although I could not find any way to correct double bonds, following command works for adding hydrogen to pdbqt files, if you ar using terminal for Open Babel:
>>obabel -isdf *.sdf -opdbqt -O*pdbqt -h
- Badges
- Science topic
- Similar topics
- Filing