Some Schiff-based metal compounds have been drawn using ChemDraw 19.0 (2D) and saved them in MDL molfile (.mol) format. They were converted to 3D using GaussView 5.0, and energy minimization was performed using Gavedit 2.5.1. However, every time I perform molecular docking in pyrx, the structures appear split or broken. What could be causing this issue, and how can it be resolved?
Once i performed molecular docking in autodock and visualized it in biovia discovery studio my output ligand was broken, later I downloaded ligand from pubchem and opened it in chimeraX and saved it in pdb format for docking the resultant ligand was not broken. As I mention you may try If you have chimeraX and free time.But I am not sure wheather it works or not. Another possible Idea may be the opening you compound in avogardo and optimize until stable configuration formed and save it in mol2 or pdb .
Faria Tasnim Megha
You can draw schiff-based metal compound in GaussView and energy minimisation as well. If you input the mol format from ChemDraw file so first of clean geometry of compounds.
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