Fedaa Ali

5 Questions 10 Answers 0 Followers

Questions related from Fedaa Ali

Why the protein moved out of the solvation box after minimization using OpenMM?

Hello, I am trying to perform MD simulation for the protein-ligand system and I got this after Minimization. I used openMM for minimization and I used ambertool for protein-ligand...

21 January 2021 2,108 2 View

How to prepare a solvated Nano-porous graphene sheet system for LAMMPS using VMD?

Hi, I am going to perform MD simulation for the Nanoporous Graphen sheet. I know how to make the pores in VMD. But when I tried to make the data file it was lacking a lot of parameters such as...

21 November 2020 3,696 2 View

How to construct mixed membrane bilayer in gromacs?

Hello, I need to perform MD simulation for a protein embedded in a mixed membrane bilayer with certain concentrations of different lipids (sqd, dgd, and mge lipids). I didn't find tutorials for...

18 October 2020 6,566 3 View

How to convert Gro files to Pdb using gromacs?

Hello, After I minimized the protein structure I used editconf in gromacs to convert the minimized GRO file to PDB. when I visualized the PDB file produced, it was totally corrupted which...

10 October 2020 873 4 View

How to solve this error "Atomtype FEJO not found" ?

Hi, I am trying to minimize the photosystem I protein complex using gromacs, and I am getting this error ' ERROR 1 [file topol_Other_chain_A2.itp, line 3339]: Atomtype FEJO not found' when...

10 December 2019 4,543 3 View