I am working on protein ligand MD in gromacs, Half of my protein is outside the box in solv.gro. How can I make them inside box?
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
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
Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer
30 July 2024 3,354 1 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 View
If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...
28 July 2024 673 3 View
Please suggest basic literature on lattice-based cryptography. A kind response from the cryptographic community will be highly appreciated.
24 July 2024 6,291 4 View
Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...
24 July 2024 367 4 View
I am performing fluorescence experiments using a ligand to detect metal ions. I want to determine the Lowest Detection Limit (LOD) using the formula LOD = 3σ / K. However, I'm uncertain about...
19 July 2024 1,086 1 View