How to solve restraint failure problem in gromacs?

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 663 3 View

How to cap a single residue in gromacs?

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 4,663 3 View

How to solve A list of missing interactions error during free energy calculation using gromacs?

31 December 2019 5,054 4 View

Why editconf removes ligand during box formation in gromacs?

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 6,078 8 View

How can I get protonation states of protein and ligand using pdb2pqr webserver with propka 3.1?

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 4,817 12 View

How to set input for minimisation in amber having protein frozen?

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 7,724 10 View

From where to find scp -r ~yuchzhou/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/rizzo_amber7.ionparms ./ ?

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 3,919 4 View

How to install Network 1.11.x version for python?

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 4,523 1 View

How to combine tpr files in MD after restart?

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 9,527 3 View

How much time required for nvt and npt equilibration in protein ligand compleax MD simulation?

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...

09 October 2018 1,073 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

Build an orthogonal box in ASE?

Hello, I was wondering the best way to build an orthogonal box filled with a defined crystal structure in ASE. I know it could be easily done in LAMMPS, but I guess it is also doable in ASE. The...

21 February 2021 5,899 4 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View