Hi everyone. I am new here and also newbie in docking study (my major is quite different) Anyone can help me with Ligplot troubleshooting?
When I try to use Ligplot plus to study/visualize molecule-target interaction, I just cant get proper binding result as I expected, only the intra-ligand binding is shown, not a interaction between ligand-receptor(target) at all
To explain how I do this, get PDB file of target (TLR-MD2 complex ; 2z64), download ligand (dexa) from pubchem and transformed into .MOL2 format
I used Swissdock (http://www.swissdock.ch/) to get docking result and downloaded the result as UCSF chimera file of proper binding pose and structure
after, using Chimera,
I did some modification in each ligand and target separately, with best docking pose,
(leave only MD2 part of target, add hydrogen, add charge..)
two model got merged into single file, .pdb format
then I load the .pdb file into Ligplot plus, the program recognize the ligand (as unknown LIG) and file is executable however, it doesn't show me any interaction between ligand-target
- why aren't there any binding between ligand-target? Is it correct what they're showing? (no binding)
- Is it okay to submit Swissdock chimera file to Ligplot plus for analysis? I tried to find but there aren't many cases of using swissdock to get docking result PDB file
- if you wanna prepare a pdb file (docking result) for Ligplot, which software/method is best? Any suggestions?
please help me out.
Thanks for all advices, questions, opinions, criticisms... anything!
