The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Wed Jul 18, 2018 1:11 am

All times are UTC




Post new topic Reply to topic  [ 1 post ] 
Author Message
PostPosted: Thu Feb 16, 2017 9:33 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Thu Feb 16, 2017 9:27 pm
Posts: 1
Hi

How are you

I am trying to dock the gold nanoparticles to the protein. I am able to form the nano.pdbqt file. But When I am running the docking simulation. Th following error occurred.

unknown ligand atom type Au
add parameters for it to the parameter library first!

I tried to add the parameters to this file. But I dont know the exact parameters for Au.
These are

Rii = sum of vdW radii of two like atoms (in Angstrom)
epsii = vdW well depth (in Kcal/mol)
vol = atomic solvation volume (in Angstrom^3) (4/3*pi*(Rii/2)**3)
solpar = atomic solvation parameter

Can any body tell me these parameters for Au or how to calculate these parameters for Au. Then I can able to run the docking Thanks

Regards


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 1 post ] 

All times are UTC


Who is online

Users browsing this forum: No registered users and 1 guest


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
POWERED_BY
Translated by MaĆ«l Soucaze © 2009 phpBB.fr