Molecular dynamics simulation?

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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

How can I solve this MD simulation problem?

I generated the complex of my protein and ligand and visualise it in Chimera and other visualisation software but I observed no interaction between my protein and ligand. What could be the cause...

21 February 2022 5,484 3 View

Molecular dynamics simulation?

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

19 February 2022 6,869 4 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

How do I replace a file with a more recent version of a paper that was uploaded to ResearchGate?

The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...

07 August 2024 9,934 3 View

How to solve g_mmpbsa error?

Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out

07 August 2024 6,066 0 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

How do you delete a duplicate pdf for the same paper on ResearchGate?

The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.

07 August 2024 9,508 1 View

AUX gas reading problem on QE with full MS and PRM method in one run?

Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...

06 August 2024 4,953 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

JCPDS 65-7246 file please?

Dear Researchers Kindly share JCPDS 65-7246 file Thanks in advance

04 August 2024 5,613 1 View

Dirty and clean?

Hi everyone I need a file with a dirty and clean potato image

04 August 2024 7,199 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

Subhamoy Mahajan

Can you provide more details, like what commands you used, what system you are working with.

Martin Klvana

Torsions are defined by four atoms (hence 4), of which the terminal ones may be wild cards (hence 2). Zero means that the torsion is undefined: add this torsion and its parameters to the force field parameter file.