How to fix an error in AutoDock related to the Grid?

15 July 2021 0 7K Report

Got the following error in AutoDock:

/cygdrive/c/AutoDock/autodock4: WARNING: Unrecognized keyword in docking parameter file. /cygdrive/c/AutoDock/autodock4: ERROR: insufficient grid points. /cygdrive/c/AutoDock/autodock4: Aborting... /cygdrive/c/AutoDock/autodock4: Unsuccessful Completion.

The grid is set according to the parameters which were chosen before for the macromolecule (that one was successful).

Also, there is another error:

ERROR: Unknown ligand atom type "Z"; add parameters for it to the parameter library first!

Could you please tell how these errors can be fixed?

Thank you.

Badges
Science topic

Similar topics
Psychology

More Sarah Bayazit's questions See All

Tips for teaching Orton Gillingham+ to students with autism?

I am beginning to use OG+ in my district and noticed during training there are a lot of materials and routines, which may be overwhelming for my students, especially those on the autism spectrum....

30 July 2024 5,695 0 View

Does anyone know where to find polypropylene microspheres or microparticles around 1-5micrometer?

These will be used for the study of microplastics in the lung

29 July 2024 9,609 2 View

Can primary care be sustainable ? And how ?

I am starting to work on this question, with particular reference to what we might be able to learn from countries outside the UK. Of course this topic is huge, and I am breaking sustainability...

25 July 2024 1,545 3 View

How do I run a dead well test for a QuantStudio 5 qPCR machine?

I am preparing to run a lot of samples on a 384 well plate and I wanted to test if any well in my PCR machine is dead so as not to lose any data. I would really appreciate help with how I can do...

24 July 2024 8,172 1 View

Looking for research articles regarding effective scholarship in EBP in nursing?

11 June 2024 1,896 4 View

To what end, Ethiopia?

Ethiopia has seen escalated civil war since 2021. Immediately after Ethiopia's PM took over power in 2018, a ceasefire and a peace agreement was signed between Ethiopia and Eritrea ending one of...

06 June 2024 6,306 0 View

Random walk vs probabilistic distribution. How to use a random walk as a probabilistic distribution.?

I am looking forward to using random walks as a probability distribution for solving a particular problem in a research field. I found some blogs and articles which states different concepts of...

26 May 2024 8,302 0 View

Looking for a full text ?

I am looking for the full text of: Pfaffenrath V, Kaube H. Diagnostics of cervicogenic headache. Funct Neurol. 1990 Apr-Jun;5(2):159-64. PMID: 2227537. Hopefully someone can help me...

22 May 2024 9,624 0 View

Using a ZymoPURE II Plasmid kit, what could cause clarified lysate to turn pink and cloudy after binding buffer addition, and result in low yield?

Hi all, I used a ZymoPURE II Plasmid Maxiprep kit to isolate plasmid DNA and ended up with very low yield and poor quality. Specifically, less than 10ng/uL in 500uL from 150mL of culture, and...

15 May 2024 6,870 2 View

How to analyse WMT?

Hello, I am a PhD student and I need a help/ resources on how to clean and analyse OSPAN working memory task data! Thank you

08 May 2024 6,649 0 View

Smart grid ideas?

How to use and this is economical?

06 August 2024 3,160 2 View

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Why Cl atom is not showing in docked comlex of molecule?

During the preparation of a ligand molecule in autodock or openbabel Cl atom is not showing in the .pdbqt file whereas it was present in the pdb and sdf file. Due to this Cl atom is not showing in...

13 July 2024 3,486 6 View

How can I deal with the error message generated while dropping pdb files on Autodock tool ?

Dear Docker community, I'm a beginner at using molecular docking, and I'm facing a problem when I want to open or drop a pdb file on Autodock tools. The folder is saved with the extension.pdb;...

05 July 2024 8,348 4 View

How to prepare proteins for multiple Ligand Docking with PyRx?

Hello everyone, I have been trying to understand the concept of performing docking for repurposing studies. I've watched a couple of tutorial videos about docking with Pyrx, but at some points, I...

29 June 2024 860 3 View

Can someone help me molecular docking using autodock 4.2.6 tool?

i'm carrying out molecular docking for a compound containing metal, Platinum, with 3T6A protein using Autodock 4.2.6 tool. However, i cannot run Autogrid to obtain .dpf file which i'm going to...

28 June 2024 7,050 7 View

Can someone recommend validation target + ligand/decoy sets for AutoDock GPU?

I'm running virtual screening tests with AutoDock GPU and am trying to validate that my configuration (parameter file, search box settings based on the target, search parameters, etc.) is correct,...

26 June 2024 6,944 1 View

How to solve this error while I simulate gidl using tcad ?

There is an error message "interface silicon/oxide not found in grid xxx.tdr file"

26 June 2024 5,551 0 View

How can I solve the problem with Autodock 1.5.7 version, Command prompt?

I follow the protocol in this paper "Computational protein–ligand docking and virtual drug screening with the AutoDock suite" for the "Flexible Docking". Everything is smooth until I write the...

22 June 2024 3,089 2 View