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Questions related from Arun Bahadur Gurung
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 7,780 0 View
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 9,483 1 View
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 8,401 2 View
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 3,316 2 View
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 2,600 0 View
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 7,735 0 View
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 3,792 3 View
