Simulated annealing in PyRx time consuming?

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What is more abundant in human cells? Beta or alpha glucosidase?

I am working on the well studied glucosidase - cancer relationship. During the work I have come across that beta-glucosidase is less abundant in cancer cells nevertheless human cytoplasm where...

09 October 2019 3,931 2 View

Suggestions for charge calculation (delocalized)?

I have modeled an oxocarbenium ion like transition state (at B3LYP/6-31+G* level of theory) with overall charge of -1. I would like to calculate and check partial charges for the molecule. So far...

05 June 2018 573 3 View

How to plot a reaction profile?

I have obtained zpe corrected energies for reactant, TS and product states. I can plot a general scattered plot using MS Excel (but not that great). I would like to know how to plot a reaction...

05 June 2018 9,206 3 View

Molecular docking/MD simulation to analyze TS stabilization?

I was able to successfully locate and confirm TS for my glycoside hydrolysis reaction. As the next step i thought performing molecular docking followed by SMD QM/MM calculation. In doing so i...

04 May 2018 2,986 5 View

How can I use spartan out files instead of gout in Amber 16?

I have been using Amber16 MD suite. As far as I have come a across respgen program in the suite only supports Gaussian output file as the preliminary input. Due to the fact that I follow Spartan...

09 October 2017 4,270 1 View

What is multiple ligand docking approach?

Can someone please elaborate me on the idea of multiple ligand docking approach and how it is done? What really can be predicted using this approch? Thank you.

01 February 2017 1,446 1 View

How to perform QM Reaction study on Enzyme Inhibition?

For MD Simulated protein-ligand complex I have extracted the ligand and the reacting residues(as mentioned in literature) for further kinetic study. I have imported this model to spartan software...

01 January 1970 9,143 7 View

What is the best way to analyze binding energy for a small molecule docked in to several snapshots?

I have run vina for 6 snapshots of pre equilibrated cystal structures with several ligands. Now I have 6 vina energies per small molecule. What is the best way to analyze and filter results? I...

01 January 1970 3,545 4 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 1,493 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 7,726 4 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,703 7 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 3,142 4 View

What are the steps of formulating a herbal extract into a sheep/goat drench?

I am working on natural remedies for de-worming in small ruminant livestocks. Part of my project involves formulation of drench-type product, which I have not much experience in. My experience is...

30 July 2024 9,806 1 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 3,083 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 672 3 View