Mohon Paul

4 Questions 1 Answers 0 Followers

Questions related from Mohon Paul

MMPBSA shows following error: "TypeError: a bytes-like object is required, not 'str'". How to circumvent this ?

I am doing md simulation of HDAC11 protein with prospective ligands. I have completed molecular dynamics production run. But whenever I am doing MMPBSA.py assay, it is showing following...

19 January 2024 6,783 1 View

How to solvate protein ligand complex with extended water model ,?

Hi everyone, I am simulating HDAC11 with my prospective ligands as inhibitor. I need to solvate the complex with SPC/E water model. But in gromacs there are only SPC, TIP3 and TIP4 water model are...

23 November 2023 9,819 0 View

How to define atom types in .pdb file ?

Hi everyone, I am trying to simulate HDAC11 with prospective ligands. As it is a Zinc containing molecule I have to parameterized it with Zn. For this purpose I am trying MCPB.py. For that case I...

25 September 2023 2,190 0 View

Is gromacs interaction energy function is enough or I have to do gmx_mmpbsa assay for better insight ?

I am going to do md simulation of 10 receptor-ligand complex. Is the gmx_energy function is enough to decide the binding strength or I have to do gmx_mmpbsa to find free binding energy ? Is...

15 August 2023 9,241 1 View