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Questions related from Larwubah Kollie
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...
30 November 2023 3,017 1 View
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...
16 January 2023 3,987 1 View
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...
22 February 2022 5,448 3 View
Why is my protein topol.top file like this? attached is the file
20 February 2022 6,838 4 View
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)?
16 February 2022 4,115 2 View
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....
15 February 2022 9,919 3 View
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...
13 February 2022 2,501 3 View
How can I use ignh to ignore water molecules in a gromacs molecular dynamic simulation?
12 February 2022 7,775 1 View
I doing MD simulation of protein-ligand interaction at two different temperatures 273K & 310K, how can I do this?
09 February 2022 644 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 the stern-volmer user-defined fitting?
10 November 2021 5,268 0 View
