15 Questions 19 Answers 0 Followers
Questions related from Subhadeep Sen
At the installation stage, after giving the command gmx_MMPBSA_test it is showing "MMPBSA_Error" and "git failed when trying to clone the gmx_MMPBSA repository". i am using gromacs 2021.3 in...
29 August 2024 5,300 1 View
I am trying to run a md stimulation in gromacs for HDAC2 inhibitor and ligand. The protein is metalo protein, contain a Zn atom. Now I am facing problem whille running the nvt.mdp file. I have...
28 June 2024 10,248 4 View
I am trying to run a md stimulation in gromacs for HDAC2 inhibitor and ligand. The protein is metalo protein, contain a Zn atom. Now I am facing problem while converting the pbd to gmx, i.e., in...
24 June 2024 8,803 3 View
I am facing this error in gromacs while making the pdb2gmx file. Can anyone help me to solve this error.
24 April 2023 6,304 0 View
I am facing this error in gromacs, can anyone help me to solve this error.
21 April 2023 3,479 3 View
What will be the best tutorial to run md stimulation on gromacs for a beginner? Can anyone help me regarding this issue.
15 April 2023 3,815 3 View
How to perform molecular docking with metal complex as a ligand in Autodock vina or Autodock software?
16 December 2022 1,074 0 View
In the Schrödinger Maestro (free version) , when I am trying to preprocess a nanostructure by assigning zero order bond in the Protein preparation option, it is showing error. Can anyone help me...
05 April 2022 5,306 1 View
What is the grid spacing that autodock vina used 0.375 or 1 angstrom? Some of the cases many have told that autodock vina used spacing 0f 1 angstrom but in some cases it is written as 0.375. So I...
22 March 2022 9,155 3 View
I was trying to do docking study with some proteins like 6LU7, 6W79 in Autodock. But every time in the time of running AutoDock after the AutoGrid, this error message is coming "error: 2137...
27 January 2022 9,432 4 View
I was trying to get the RMSD score of the protein having a ligand with the same protein after docking with that ligand. But getting zero score every time in Pymol. How to get rid of this problem?...
26 January 2022 1,645 6 View
I am trying to dock a ligand with protein 6LZG. But, being a newcomer in this docking field, could not get the active sites of that protein. So, Can anyone provide me the active sites of 6LZG...
22 January 2022 2,942 11 View
I was tried to dock Cucurbit[7]uril with protein in Autodock vina, but the ligand structure i.e., the structure of Cucurbit[7]uril was planar (taken from the pubchem or other website everywhere...
20 January 2022 2,313 3 View
Is there any method available to determine the binding stoichiometry between a metal and a ligand, if the molecular weight of the ligand is not known? I know about job's plot and mole ratio...
28 September 2021 8,584 3 View
I have synthesized SnFe2O4 nanoparticles by coprecipitation method. Which should have same structure as Fe3O4. But the XRD result is surprising, it is showing that the highest intensive peak which...
15 July 2021 5,748 18 View
