Biomedical Research Institute of Malaga (IBIMA)
Question
Asked 4 June 2015
Does anyone know about molecular docking studies for silver nanoparticles?
Need to do molecular docking studies for silver nano particle synthesized by green synthesis against anticancer using Dalton's Lymphoma Astices from male swiss albino mice any one has idea or ref articles or institutions where it can be done in india
All Answers (2)
Similar questions and discussions
Preparing a ligand for docking using UCSF Chimera messes up the bond order of the ligand
- Sarthak Mohanty
Hello!
I want to perform a MD simulation of a protein-ligand system after performing a molecular docking using the Autodock Vina plugin of UCSF Chimera.
When preparing the ligand for docking (using the "Minimize Structure" module of Chimera) I noticed that the bond order of two carbon atoms get messed up and both carbons end up becoming hypervalent (valency = 5).
This is causing problems further down the line when I try to parametrize the ligand using CGenFF or SwissParam for the MD simulation.
This is the 2D structure of the ligand before preparation (https://drive.google.com/file/d/1-_9RFXtP_uz2WQTaYb0t9myDJtgo1Pxd/view?usp=sharing).
This is the 2D structure of the ligand after preparation (https://drive.google.com/file/d/1Xf2xr1b_a-KXFEtNRsFaI-j--09TrikL/view?usp=sharing)
The ligand file is originally in SDF format which Chimera converts to MOL2 format during the preparation.
I am attaching the SDF and MOL2 files here as well. I hope it helps anyone who kindly looks into this issue.
I don't know what is causing this issue and I don't know how to fix it.
Any help/advice will be greatly appreciated.
Thank you.