Ekrem Yaşar

9 Questions 5 Answers 0 Followers

Questions related from Ekrem Yaşar

How can we complete the missing residues in crystal structures?

Hi everyone, Are there any other alternatives other than the MODELLER program that I can use to complete the missing residues in the crystal structures before running the simulations? We can...

19 December 2023 9,997 3 View

Gromacs Equilibration Error?

While trying to run the MD simulation with the CHARMM-GUI input file, I encounter such an error during the equilibration phase. How to overcome this? gmx mdrun -v -deffnm ${istep} Program:...

26 May 2023 9,932 4 View

Analyzes with Gromacs outputs on the Schrödinger Maestro SID panel?

How can I perform ligand-protein interaction analysis (L-P contact) using Gromacs .gro and .xtc outputs on SID (simulation interaction diagram) panel in Schrödinger Maestro version 2022.4? After...

22 March 2023 3,259 0 View

How can I identify interactions of binding site residues of a GPCR?

I am trying to calculate protein-ligand contacts (especially hydrophobic interactions) in the allosteric site of a GPCR. Thus, could you suggest a tool that I can use free of charge, except...

27 February 2023 8,141 4 View

How to convert Gromacs files to Amber output files?

I want to use cpptraj for some analysis but I need to convert my topology and trajectory files from Gromacs xtc, tpr format to Amber nc and parm formats. Could you please let me know how can I...

26 February 2023 3,013 2 View

How can calculate an MM-PBSA or MM-GBSA for the latest GROMACS versions (2020.5)?

Hi everyone, I am trying to calculate MM-PBSA or MM-GBSA for ligand-protein structures in my simulations with GROMACS 2020.5. version. There are recommended calculations for older versions of...

23 February 2023 7,966 4 View

What are the effects of water molecules on the ligand binding package?

Hello everyone, What tools should I use to determine the effects of water molecules on ligand binding sites for protein-ligand interactions? (Especially in MD simulations for ligand interactions...

29 March 2021 5,439 1 View

Is there any modeling application?

Can I model the change in the magnetic field applied to an ion channel? Is there any modeling application? - Can I model this change if a conformational change occurs in the structure of the...

02 July 2018 2,911 1 View

GPCR activation mechanism?

When we consider the active and inactive structures of a GPCR when describing its activation mechanism, is it sufficient to talk about the change of the distance between TM3-TM6 (macro-switches)...

01 January 1970 5,954 0 View