Hi. what kind of charges do I add to my macromulecule in autodock tools software?

More Heidarali Panahi's questions See All

How should I dispose expired dehydrated culture medium?

Is there any refrence?

05 November 2023 6,807 1 View

Gamma sterilization of borosilicate glasses?

Hello, we need to sterilize borosilicate made transparent glass vials with gamma radiation (15 or 25kgray). Question 1: Do these glasses discolor after radiation? Question 2: Does this...

23 October 2023 1,731 0 View

Why does the expression of P53 and Bcl2 genes increase simultaneously?

In our experiment, we are checking and comparing two synthetic chemical compounds' impact on the expression levels of apoptotic and proto-oncogenic genes including p53, Bcl-2, cMyc, hTERT, and...

03 August 2022 1,467 2 View

Decreased size of nanoparticle with increasing concentration?

Hi there, I have synthesized selenium nanoparticles coated with different concentrations of chitosan folate polymer, but based on dls and fesem, the size of nanoparticles coated with chitosan...

03 October 2021 5,919 1 View

Decreased size of nanoparticle with increasing concentration?

Hi there, I have synthesized selenium nanoparticles coated with different concentrations of chitosan folate polymer, but based on dls and fesem, the size of nanoparticles coated with chitosan...

03 October 2021 4,826 1 View

Decreased size of nanoparticle with increasing concentration?

Hi there, I have synthesized selenium nanoparticles coated with different concentrations of chitosan folate polymer, but based on dls and fesem, the size of nanoparticles coated with chitosan...

19 September 2021 5,893 3 View

Sterile chitosan folat polymer?

Hi, I want to start my cell culture to run a MTT assay , how can I sterilize my polymer?

15 December 2020 2,053 1 View

Solving chitosan folate nanoparticles in dmem?

Hi there, I have been struggling with solving my chitosan folate coated nanoseleniums in dmem culture media sincr it is only soluble in acetic acid , and hardly soluble in basic media. What can I do?

19 November 2020 5,844 3 View

TEM and SEM of chitosan coated nanoselenium?

Hi, I have a 25 ml sample of chitosan coated nanoselenium with average diametere of 112 nm, considering the fact that chitosan after being kept in water media swelles, how can I send a sample for...

08 November 2020 7,059 3 View

Addition of glycerol in measuring zeta potential?

Hi there I wanted to know if it is ok to add 2 or 3 drops of glycerol for suspending the nanoparticles in water before measuring the zeta potential?

26 October 2020 2,362 3 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

Please explain how the plastic input value should be considered from the true stress-strain curve for the bilinear elastoplastic material model ?

I am working on Abaqus/Explicit(Quasistatic ) for the deformation of the auxetic structure model. Please explain how the plastic input value should be considered from the true stress-strain curve...

05 August 2024 454 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Is it necessary to covary exogenous constructs in a structural model?

I am working on a SEM model where i have 7 latent variables (6 exogenous and 1 endogenous). In AMOS when I co-vary the exogenous constructs, only 2 paths are coming significant out of 6. But when...

03 August 2024 6,028 4 View

In SEM, if a latent variable consists of three observed variables, and each observed variable has four items, what should I do?

Suppose I am studying the construct of "Academic Motivation" (latent variable) in students, which is measured through three observed variables: "Intrinsic Motivation," "Extrinsic Motivation," and...

31 July 2024 3,913 6 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 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

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

28 July 2024 4,762 2 View

Bootstrapping in SEM Amos ?

Can a researcher use small sample size of 40 while using SEM with bootstrapping of 1000 and is it possible to get published

28 July 2024 4,402 2 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

Yoshinobu Ishikawa

Hi Heidarali,

If you are going to try AutoDock Vina, either will be OK, because Vina ignores receptor's charges for scoring.

For AutoDock 4, I recommend both. After several docking, you should carefully check your results with your experimental data.

Aditi Gangopadhyay

I wonder if the FAQs (question 2) of this document would be of help: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-with-autodocktools/UsingAutoDockWithADT_v2e.pdf

Fortunatus Chidolue Ezebuo

kollman for macromulecule and gasteiger for ligand but since your ligand is a peptide, you should add kollman to the ligand as well.

Heidarali Panahi

thank you very much dear friends.

Always welcome.