Protein-Ligand Complex was generated after performing site-specific docking in AutoDock 4.2.
I am following the MD-Tutorials by Justin Lemkul.
Often bulky antibiotics are administered for therapeutic purposes. For building topologies for protein and ligands, both are separated using the 'grep' command.
When the ligands are visualised in Avogadro, sometimes the ligands seem broken or distorted thereby unfit for topology building.
I'm Using GROMACS 2020.1, CHARMM force field (Feb 2021), CGenFF server for building ligand topology.
Kindly provide some suggestions to resolve the issue.
Thanking you in advance
Hi,
Do not use Avogadro. I would recommend you to open the .pdbqt file in PyMOL and save the desired pose in .mol2 format in order to submit it to CGenFF server.
You can also open protein-ligand complex in PyMOL to verify if the complex is still good.
With the grep command you are separating the coordinates of the atoms from a pdbqt format without taking into account the unions. I recommend that you isolate separate the model of interest from your pdbqt and use openbabel to generate any other format.
Hi Researchers,
After 1 year of intense research on molecular dynamics simulation, myself and my team was able to troubleshoot the issue. I'll summarize the steps in a few points...
1. Use 3D ligand coordinates for performing molecular docking analysis
2. If Avogadro is throwing some errors, UCSF Chimera is another powerful standalone tool that can also be used for satisfying its valences and saving the optimized structure in desired MOL2 format
3. If the problem still persists, I personally suggest performing quantum chemical optimization simulation for the ligand before subjecting to molecular docking analysis
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