How can I generate angle restraints using gromacs?

26 September 2020 0 1K Report

The system that I am working on contains two ligands with a protein and I want to use angle restraints between water molecule and amino acid residue along with the distant restraints.Is there any command line to generate angle restraints or any script that I can use?.

Appreciate if anyone helps

Thanks

Badges
Science topic

More Virangi Hewage's questions See All

Have you ever got high backgrounds in western blots done with heart tissues ?

Hi, I am doing WB with heart tissues (Rat) these days and having a problem of high background. We have no issue of getting high background for WB done with cells or other tissues, the protocol is...

11 June 2019 2,726 3 View

What are the essential cofactors to perform in vitro assay using alpha/beta hydrolase enzyme ?

Need to perform in vitro reaction with substrates and purified protein (Methyl esterase/alpha/beta hydrolase super family) 1. What are the essential cofactors? 2. Which buffer solution/pH should I...

14 April 2019 9,298 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

Chlorinated organic formation in odor control scrubbers using hypochlorite?

I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...

03 March 2021 3,661 2 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

Ester cleavage conditions?

Hi all, I need to cleave the ester in Ethyl 2-amino-1H-imidazole-5-carboxylate to make the carboxylic acid and retrieve the product from solution to use in downstream applications of linking to...

01 March 2021 8,766 3 View

How to remove DCU and HOBT from my reaction?

I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??

28 February 2021 2,153 1 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

What is the most common number of epitopes in an multi-epitope Vaccine?

hi everyone, I'm interested in the field of vaccine design specifically multi-epitope cancer vaccines , I want to know if there is a minimum and maximum number of epitopes we could use in a...

27 February 2021 3,882 3 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 increase solubility of Poly acrylic acid in Dioxane solvent?

I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...

25 February 2021 2,225 5 View