[Chimera-users] Using iBabel to convert Chimera's pdb to pdbqt

Elaine Meng meng at cgl.ucsf.edu
Sat Sep 19 10:05:01 PDT 2020

Hi Jatin,
I already answered your question of how to get a pdbqt file from Chimera.  You would do it via the Autodock receptor prep script (included with Chimera), or get the receptor prep script from the Autodock website and run it yourself directly outside of Chimera.  Here are the posts:


It is unclear why you want your complex all in one file.  As far as I know Vina would want a separate file for the receptor and a separate file for the ligand.

Since you have decided to try some other method than Chimera, this mailing list is probably not the best place to ask your question.  I don't know if there is any iBabel help, but maybe you could try the Vina mailing list.


Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 19, 2020, at 9:32 AM, Jatin Kashyap <jk435 at njit.edu> wrote:
> Dear UCSF Chimera Community,
> I am trying to minimize a complex[1] and saving it in a pdbqt format. I minimize it in Chimera and saved in pdb[2], followed by using iBabel (GUI of open babel for Mac) to convert pdb into pdbqt. 
> Here are two things: first, if I convert without using any flag then output gives me pdbqt file with BRANCH information which is not supported by Vina. To solve it I am using -XR flag in iBabel to trim the BRANCH information so that resulting pdbqt file can be read by Vina. But in that case iBabel is giving me weird looking structure and upon inspection of pdbqt file[3] I realized the complex was split into different models. I had successfully followed the same workflow for other minimization code i.e. YASARA. Can anybody please help me to fix it.
> I am attaching files below with corresponding citations.
> Thank you.
> [1]
> <7bv2_rna.pdb>
> [2]
> <7bv2_rna_rel.pdb>
> [3]
> <7bv2_rna_rel.pdbqt>
> ——
> Jatin Kashyap 
> Ph.D. Student
> Dr. Dibakar Datta Group
> Department of Mechanical and Industrial Engineering
> New Jersey Institute of Technology (NJIT)
> University Heights
> Newark, NJ 07102-1982
> Phone- (201)889-5783
> Email- jk435 at njit.edu
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