How can I solve this MD simulation problem?

More Larwubah Kollie's questions See All

Hi everyone, can I download amber99sb-ildn force field in gromacs?

I want to download the amber99sb-ildn force field in gromacs to study a protein-ligand interaction using a serum protein and a TCM as a ligand, but the field cannot be seen on the gromacs tutorial...

29 November 2023 3,048 1 View

Hi everyone, why are my genes clustered like this in Cytoscape?

I want to visualize the common genes generated from the string database. When sent directly from the String database for visualization my genes are clustered so tightly that I can not tell which...

15 January 2023 4,002 1 View

Molecular dynamics simulation?

Why is my protein topol.top file like this? attached is the file

19 February 2022 6,869 4 View

Molecular dynamics simulation?

how can I fix this error in gromacs, ERROR 37 [file ligand.prm, line 41]: Incorrect number of atomtypes for dihedral (0 instead of 2 or 4)?

15 February 2022 4,142 2 View

How can to fix gromacs solvation error?

I have the ligand perimeter in my working folder and file but I am receiving an error in gromacs that says "Fatal error: Topology include file "ligand.prm" not found", how can I fix this, please....

14 February 2022 9,952 3 View

How can to fix this ions.mdp file is not accessible in gromacs?

How can to fix this? In command-line option -f Invalid command-line options File 'ions.mdp' does not exist or is not accessible. The file could not be opened. Reason: No such file or...

12 February 2022 2,518 3 View

How to fix additional hydrogen in gromacs??

How can I use ignh to ignore water molecules in a gromacs molecular dynamic simulation?

11 February 2022 7,801 1 View

How can I increase the temperature in Molecular Dynamics simulation?

I doing MD simulation of protein-ligand interaction at two different temperatures 273K & 310K, how can I do this?

08 February 2022 686 4 View

How can I create user-defined function using stern-volmer equation(Fo/F=1+Ksv[Q]) in originlab software. what are the parameters needed to build it?

How can I create user-defined function using stern-volmer equation(Fo/F=1+Ksv[Q]) in originlab software. what are the parameters needed to build the stern-volmer user-defined fitting?

09 November 2021 5,292 0 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

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 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

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

Shaban Ahmad

Dear Larwubah Kollie

Did you've activated the complex interaction (P-L) in the software are you using.

If its still not working try with Maestro Free (Schrodinger LLC) to visualise the complex and hopefully your problems will be resolved.

Sutanu Mukhopadhyay

Try to visualise it with any one of the following:

1) Discovery Studio Visualizer (https://discover.3ds.com/discovery-studio-visualizer-download)

2)PLIP Server (https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index)

3) Ligplot+ (https://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html)

Debarati Dasgupta

When you say interactions, have you seen the ligand atom distances from the protein. Have you used any modeling tool for designing the complex? Or was it docking?