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

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

Why nvt equilibration starts from step zero after a restart?

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 1,107 1 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

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 2 View

Does anyone know to clarify these changes?

01 March 2021 1,290 2 View

How can I convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 View

How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials?

Hi, all! How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials? I have not find the choice for explicit element in Abaqus CAE. I am wondering whether it is possible...

25 February 2021 9,936 2 View

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25 February 2021 5,713 1 View