Why are there broken bonds in ligand pdbqt out file in PyRx Auto Dock Vina?

More Supriya Hakeem's questions See All

How to calculate dosage for cell culture treatment by using plant extract ?

how to calculate dosage for cell culture treatment by using plant extract ?

12 May 2024 7,335 1 View

Can anyone recommend a company that does LC-MS/MS for silver stained gels where I can outsource my samples for proteomics analysis?

Looking for most cost-effective manner to outsource my samples (silver stained gels) for proteomics analysis using LC-MS/MS. If anyone has outsourced samples outside or in INDIA for LC-MS/MS and...

21 April 2024 309 2 View

How to check whether the qPCR primers degraded or not?

I had transformed my desired gene along with selectable marker into rice plants and started with gene expression studies. Previously Amplification was observed in both genes but now on repetition,...

14 March 2024 7,841 1 View

Which software is the best for studying root architecture in plants?

Hi, Is there any free application I can use to study root morphology? The following information would be helpful to me: primary and lateral root lengths, root density, and root area. Thank you

11 January 2024 6,401 2 View

What could be the cause of getting such blots?

my protein is a nucleolar protein which is tagged with HA, FLAG and myc tag. i have over-expressed it and good GFP expression was observed which is directly proportional to the amount of my...

11 January 2024 2,057 2 View

Why C4 minor millets, even under good management do not out yield C3 rice ?

Despite having negligible photorespiration and photosynthetic advantages, what are the factors or reasons that C4 minor millets failed to surpass the yield of C3 rice ?

10 December 2023 702 1 View

How to obtain permission for translation of scale?

How to obtain the permission from original author for translation of scale?

27 September 2023 7,521 2 View

Anybody have idea about orange node in multicut forage pearl millet?

I want to know about the orange node and brown mid rib traits observation in forage pearl millet

06 September 2023 3,220 0 View

How to calculate regeneration ability in forage pearl millet?

I have data on number of tillers,number of tillers at both cuts and tillers regrown i need any supporting paper and supporting answer whether there exact formula like that

06 September 2023 2,756 0 View

Can anyone help me to know how we can study oil-in-water or water-in-oil emulsion using optical microscope?

While removing the emulsion from the container, the layer is getting disturbed. I read few papers that say we have to put a drop our sample on glass slide and dry it. Can anyone please help me?

20 August 2023 5,506 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

How to estimate a protien's size using Chimera or PyMol? how correct this estimated can be?

I need to know the approximate size of my target protein for Negative-stain EM. I have an alpha-fold predicted structure of the protein. I do not see any turtorial on internet for estimating the...

21 July 2024 5,732 3 View

Printing residues in an object in Pymol?

Hi! I am currently working on a protein where I have selected residues within 10A of its bound ligand in pymol. However, I can not find a way to print out what residues are contained in that group...

15 July 2024 1,727 1 View

How can we identify (in silico) the interacting amino acid residues or the nucleotides involved in the Protein-Protein / Protein-RNA interaction?

Hello! everyone, I am trying to study in silico Protein-Protein and Protein-RNA interactions. Now, is there any tool with which I can identify the interacting amino acid residues or the...

14 July 2024 950 2 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

Is PyMOL good for conformational editing of a protein structure?

I'm trying the edit the orientation of some side chains in a homology protein model I made. Can I use PyMOL for such tasks? If so, could anyone navigate me to some online tutorials? If not, what...

01 July 2024 4,409 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

Lukas Schulig

Could you please upload your input files? I think there is an error within your ligand file.

Supriya Hakeem

Thank You Lukas !!!

The version of PyMOL was the problem , newer versions do not support viewing the the pdbqt files.When opened it in PMV ,(part of MGL tools) was able to visualize !!!