Citra Hasanah

5 Questions 7 Answers 0 Followers

Questions related from Citra Hasanah

I can't i install gmx_MMPBSA environment in my linux system. the process always got killed in the middle. any idea why?

i use this command: conda env create -n gmxMMPBSA --file env.yml and after waiting is always got killed like this: Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting...

17 January 2024 2,306 1 View

How to calculate binding free energy from gromacs trajectory using g_mmpbsa tools?

I was performing free energy calculation using g_mmpbsa tools. From the summary data i got the value of binding energy, but when i check the output file, it shows only data energy for the complex....

28 November 2023 4,588 3 View

Does the unfavorable bump between ligand and protein docking interaction affects the md simulation result?

I have docked several ligand and protein and few of them have an unfavorable bump interaction. When we dock protein and ligand in Autodock-vina, they give us several output like out_ligand_1,...

30 August 2023 365 3 View

What possibly a problem if i got a very high RMSD value more than 1 nm? (>10A) meanwhile it supposed to be lower than 0.2 nm or 0.3 nm?

I have run a MD simulation of complex protein SIB1 (PDB ID: 7EAU) with several small molecules (ligand) using GROMACS and all of them show huge value of RMSD. Here i attached a google drive for...

09 August 2023 7,350 10 View

I got an error message when using python cgenff in gromacs, what should i do to solve this?

the command: python3 cgenff_charmm2gmx_py3_nx2.py UNL1 UNL_fix.mol2 UNL_fix.str charmm36-jul2022.ff error message: Traceback (most recent call last): File "cgenff_charmm2gmx_py3_nx2.py", line...

02 August 2023 4,826 2 View