I am running a protein ligand complex MD simulation for 10ns. My question is how much nvt and npt simulation time is required before running production run?I am new to MD and gromacs, Any suggestion will be more than welcome.
Dear Gromacs users I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ;...
01 February 2020 873 3 View
Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type...
01 February 2020 4,757 3 View
Dear researchers I am facing this error during the free energy calculation of protein-ligand for which I have applied restrained to some atoms of protein residue and ligand. A list of missing...
31 December 2019 5,291 4 View
Hi Gromacs users I am trying to set a protein-ligand system in gromacs for MD simulation. I took topology and gro file from an external source. Now I combine the gro file of ligand and protein...
10 November 2019 6,243 8 View
Dear researchers Need your expert suggestions please. I am trying to get protonation states of my protein ligand by using pdb2pqr webserver version 2.1.1. However; when I get result propka file...
07 August 2019 4,988 12 View
I want to run MD simulation of my protein that is 479 a.a long. I found 6 bad contacts in my protein by the process mentioned in tutorial....
04 May 2019 7,857 10 View
I am following amber tutorial with HIV protease Can any one suggest me from where I can find this particular file?mentioned in this command Copy parameters of ions to your working directory...
03 April 2019 4,044 4 View
I am trying ligand protein gromacs tutorial for my protein ligand MD when I come to the command python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-nov2018.ff it says that This script...
03 April 2019 4,756 1 View
I started protein ligand MD simulation in gromacs for 10ns. However due to cluster shutdown I had to restart it again. Md.tpr file of md is formed but it do not include portion after restart; How...
01 February 2019 9,807 3 View
I am running a protein ligand MD simulation using gromacs. I have started npt equilibration for 500000 nsteps (1ns). After a computer shutdown at 170500, I started restart using following...
09 October 2018 1,202 1 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...
03 August 2024 3,589 3 View
I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...
03 August 2024 1,370 1 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer
30 July 2024 3,354 1 View