ligand losing from macromolecule when converting to pdbqt

Python Prescription - Virtual Screening Tool

[PyRx is no longer developed at MGL]

Moderator: sargis

Forum rules
[PyRx is no longer developed at MGL]

ligand losing from macromolecule when converting to pdbqt

Postby hsyutt » Fri Apr 26, 2013 8:02 am

My macromolecule contains two ligands. I used PyRx to dock the ligand A (in mol2 form) first and add the best docking result to the apo-protein. Then I used this result as the target to do the second step docking. But ligand A was missing from macromolecule when converting to pdbqt. I think there must be some problems with the input file form.
The pdb form of ligand A saved from docking result is like this:
ATOM 1 N Und d efin -13.661 -41.031 0.022 0.00 0.00 XXXX N
What should I change?

Does anyone have experience with this problem?

Thank you very much!
Last edited by hsyutt on Sat Apr 27, 2013 1:43 am, edited 1 time in total.
User avatar
hsyutt
Millimolar User
Millimolar User
 
Posts: 1
Joined: Fri Apr 26, 2013 7:15 am

Re: ligand losing from macmolecule when converting to pdbqt

Postby sargis » Fri Apr 26, 2013 5:05 pm

Thank you for the post. I've implemented a new feature in the latest 0.9 version of PyRx that let's you keep ligands when making macromolecule pdbq - http://sourceforge.net/apps/trac/pyrx/roadmap. You can make pdbqt with ADT and replace the one PyRx created if you are using older version of PyRx. Right-click on the pdbq under Molecules panel and select Properties option to see where this pdbqt is stored on your system.

Thank you for using PyRx!
User avatar
sargis
Picomolar User
Picomolar User
 
Posts: 583
Joined: Fri Oct 17, 2008 10:39 pm


Return to PyRx

Who is online

Users browsing this forum: Bing [Bot] and 2 guests

cron