Comments (4)
Hi @YvetteJxy, the problem was caused by your ligand PDBQT file, which doesn't have valid 3D coordinates but all 0s. You might want to review your procedure for ligand preparation.
If I guessed your ligand right and you generated it with obabel, here's how you could generate a PDBQT with coordinates and charges (although not necessary for vina) with obabel:
./obabel -:"C[S+](C)CCC(=O)[O-]" -o pdbqt --gen3d
REMARK Name =
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and S_2
REMARK 2 A between atoms: S_2 and C_3
REMARK 3 A between atoms: S_2 and C_4
REMARK 4 A between atoms: C_4 and C_5
REMARK 5 A between atoms: C_5 and C_6
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL 1 3.420 -1.521 0.625 0.00 0.00 +0.283 C
ENDROOT
BRANCH 1 3
ATOM 2 C UNL 1 1.153 -0.143 0.096 0.00 0.00 +0.340 C
ATOM 3 S UNL 1 2.913 -0.014 -0.300 0.00 0.00 -0.016 S
ATOM 4 C UNL 1 3.321 1.174 1.001 0.00 0.00 +0.340 C
ENDBRANCH 1 3
BRANCH 1 5
ATOM 5 C UNL 1 4.918 -1.736 0.537 0.00 0.00 +0.106 C
BRANCH 5 6
ATOM 6 C UNL 1 5.385 -2.974 1.303 0.00 0.00 +0.046 C
ATOM 7 O UNL 1 6.631 -3.182 1.245 0.00 0.00 -0.550 OA
ATOM 8 O UNL 1 4.496 -3.633 1.911 0.00 0.00 -0.550 OA
ENDBRANCH 5 6
ENDBRANCH 1 5
TORSDOF 3
from autodock-vina.
Hi @YvetteJxy, Your upload appears as a HTML file (it looks very like the login page of Jupyter server). Let us know if you reshare the files.
One more thing about --autobox
, in this scenario (a docking search), --autobox
doesn't actually set the grid size or the grid center (?). --size_x --size_y --size_z
are necessary even with --autobox
, and if not specified the center seems to be 0,0,0. Not sure if this is related to the error.
from autodock-vina.
Thank you for your help! I am very grateful for that!
I have uploaded the file again and I hope this time it will work!
files.zip
from autodock-vina.
@rwxayheee Thank you for your help! I think I know what the problem is! I didn't generate valid 3D coordinates of my ligand and now I have corrected my error! Thank you very much!
from autodock-vina.
Related Issues (20)
- Error on running prepare_flexreceptor.py for flexible docking HOT 8
- Charged ligands and receptors HOT 2
- FLexible Autodock HOT 1
- Method to capture receptor structure state after flexible docking HOT 7
- Virtual screening using Python bindings HOT 22
- Autodock Vina Scoring Functions HOT 3
- How to perform docking of drugs that contain metal ions?
- REMARK VINA RESULT not in PDBQT output of `--local_only` or `--score_only` type of calculations
- Zn docking-Chelation issue HOT 9
- An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
- Discrepancy Between Multi-Ligand Docking Score and Summed Individual Scores in AutoVina HOT 6
- Multiple-ligand docking pose PDBQT cannot be (re)scored HOT 1
- What kind of file is the Linux download? HOT 2
- ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects HOT 13
- `!pip install vina` failed in Google Colab, with a Linux Python 3 Google Compute Engine backend HOT 8
- ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects - MacOSx HOT 1
- autodocking tools HOT 1
- unknown option protein HOT 6
- Logic setting for simultaneous docking of multiple ligands HOT 1
- Covalent docking of Inhibitors to crystal HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from autodock-vina.