HOW TO Convert PDB TO PDBQ

More Lana Abid Mansor's questions See All

Is there any gene present in our body that did not came from our parents?

All I want to know is whether it is feasible or not. How did genes come to be if they do not come from parents?

12 July 2024 7,221 1 View

Which one is the most potential target for Colorectal cancer?

In 2024, which one is the most significant target for CRC drug discovery?

01 June 2024 703 2 View

Is there any inheritable capabilities of artificial DNA base pairs exist?

I'm curious about the potential of synthetic DNA base pairs in transmitting traits from one generation to another and functioning as genes that express traits. I've discovered that synthetic base...

01 June 2024 8,356 0 View

What is Brain Natriuretic Peptide (BNP) Test? why this important ?

Is this good marker to diagnose heart attack? if yes how?

26 May 2024 3,703 2 View

What type of organic molecules are suitable for fabrication of OTFT (Organic thin film transistor )device ?

I am designing some donor-acceptor-acceptor type compound . I am check their electron mobility and the nature of organic semiconductor either n-type or p-type. what type of organic semiconducting...

01 April 2024 1,521 0 View

How to analyse the pixel densities on developed X-ray film after conducting the Proteome Profiler Mouse Cytokine Array Kit, Panel A?

Hello everyone, I am seeking guidance on the analysis of scanned films obtained from Proteome Profiler Mouse Cytokine Array Kits, specifically focusing on the quantification of dot intensity using...

23 March 2024 1,341 2 View

What is the best way to label macrophages to look at them under the microscope?

Which fluorescence markers are best to use for staining macrophages. I want to prepare sample to get training with the microscope for my research.

27 February 2024 7,934 9 View

I am looking for someone who has done computational research on NON SMALL CELL LUNG CANCER & used MOE docking software?

I have selected 100 proteins from the literature on nonsmall cell lung cancer but I am having trouble in finding exact PDB IDs of it. what is the best way to get authentic PDB IDs? and secondly...

27 January 2024 3,402 2 View

Optimum sample size for data collection?

Dear researchers , Greetings. I am trying to collect data from an organization. Suppose , the number of employees in an organization is 1000. What could be the optimum number of sample size from...

26 January 2024 6,480 5 View

The XRD peaks at 44.64, 65.04, 77.04, 78.16, and 81.24 represent which forms of PVDF?

XRD measurements revealed distinct peaks at 44.64, 65.04, 77.04, 78.16, and 81.24 for PVDF membrane. Despite an exhaustive review of the existing literature, no conclusive information pertaining...

26 January 2024 7,657 5 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 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

Is it possible to dock more than one drug in the same active site or pocket of a protein to study synergistic/antagonistic/additive properties?

I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...

28 July 2024 7,413 6 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Merwyn Franco Dcosta

You can use Openbabel for conversion or MGL tools

Shafiya Sakina

MGL tools is the easiest way to convert PDB to PDBQT or u can use Openbabel install it via conda and it will convert it in one line code obabel input.pdb -O output.pdbq --partialcharge gasteiger replace input.pdb file with your actual file and done.

Harvinder Singh

If it is a Ligand/small molecule, then use openbabel. If it's a protein then use MGLtools.