I faced a FATAL error while preparing Docked Proteins for MD simulation using Amber20.
But this error does not occur while performing with non-docked protein structures. Is this problem is due to Autodock?
Use docked ligand molecule (you have to convert one docked conformation from PDB to PDB file format) and merge with protein's PDB file not PDBQT file.
USE PDB FILES FOR BOTH RECEPTOR and LIGAND.
Kiran Lokhande
Dear Sir, I have converted the file into PDB from PDBQT. After that, I faced a problem.
While running the following code, I got an error.
saveamberparm REC protein.rec.gas.leap.prm7 protein.rec.gas.leap.rst7
But, this error did not occur while performing with the Non-Docked(Structure retrieved from PDB) Protein structure.
Hi Jagadeesha,
The following tutorial can help you:
http://ringo.ams.stonybrook.edu/index.php/2018_AMBER_tutorial_with_1c87
- Badges
- Science topic