Arun Bahadur Gurung

7 Questions 6 Answers 0 Followers

Questions related from Arun Bahadur Gurung

How to computationally build hydrophobic and hydrophilic self-assembled monolayers (SAMs) for MD Simulations?

Dear All, We wanted to build computational models of hydrophobic and hydrophilic self-assembled monolayers (SAMs) for MD Simulation experiments. There are a few papers where the simulation...

14 June 2023 7,787 0 View

How to solve the error “water molecule starting at atom 44884 cannot be settled” in GROMACS v.5.1.5?

Dear All, While running protein-peptide simulation in GROMACS v.5.1.5, I am getting the following error in the MD production run step after 198 ps. “Step 93128: Water molecule starting at atom...

13 November 2022 9,489 1 View

Is there any way to resolve "Segmentation fault (core dumped)" issue while running g_mmpbsa latest version v1.7.1?

Dear All, While running the latest g_mmpbsa v1.7.1 in GROMACS 2020, I am constantly getting "Segmentation fault (core dumped)" error. I guess it's not an issue of memory. Kindly suggest some ways...

02 November 2022 8,411 2 View

How do we place molecules orderly in a simulation box in GROMACS?

Dear all, We need to pack a simulation box of cubic shape with molecules A and B such that a single protein molecule A lies in the centre of the cube and ‘N’ number of B molecules around A spaced...

24 September 2022 3,326 2 View

What are some free tools or server to adjust the torsion angles in a given cyclic peptide?

Dear All, I recently attempted to use Chimera tool to adjust the torsion angles in a given cyclic peptide but unfortunately it showed an error "Cannot rotate a bond that is part of a closed...

19 August 2022 2,610 0 View

What are some computational techniques to study the interactions between a membrane protein and peptides with acyl moieties and unnatural amino acids?

Given that there are several free software and web servers for performing protein-peptide docking, the majority of these available tools are typically not parameterized for docking peptides...

07 August 2022 7,743 0 View

How to keep the two strands of DNA together during MD simulation?

Dear All, I performed MD simulation for DNA-ligand complex for 20 ns using GROMACS v.4.6.5. with AMBER 99SB force field. The ligand topology was obtained using AmberTools 14. The results of RMSD...

15 January 2016 3,799 3 View