The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Fri Jan 19, 2018 7:24 pm

All times are UTC




Post new topic Reply to topic  [ 1 post ] 
Author Message
PostPosted: Mon Jan 06, 2014 4:06 am 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Mon Jan 06, 2014 3:35 am
Posts: 1
Hi all,

Sorry that this may be a question asked many times, but after searching in the mailing list and internet, I am still unsure about how to handle this, so I hope to get a confirmation from here.

When there is metal ions like Zn, Ca, Na, etc. in the protein pdb file, prepare_receptor4.py complains:

Sorry, there are no Gasteiger parameters available for atom 1ps3_protein: : Zn1:Zn

However, the ion is at the active site and I suppose that it is important for the binding. What should I do such that Autodock Vina will include it in the calculation?

Many thanks.

Corina


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 3 guests


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