How long does ATB server take to process the molecule submitted and give back the parameters ?

More Gauri Thapa's questions See All

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

10 February 2021 4,170 2 View

How to include MG topology information using pdb2gmx ?

I have a molecule with MG ions in the pdb file. When I am creating topology file using pdb2gmx, it does not recognize the MG ions (with gromos 54a7 ff). So I created pdb with only protein atoms...

23 January 2020 1,140 2 View

How to check the parameters generated by ATB for ligand molecule in gromacs?

I have generated parameters for Doxorubicin using ATB server to be used with gromacs. I have calculated solvation free energy of doxorubicin (parameters generated by ATB) which gives a value...

31 December 2019 6,058 3 View

How long does ATB server take to process the molecule submitted and give back the parameters ?

Can anyone give me a rough estimate of time it takes for ATB (gromacs)server to give the parameters for the submitted molecule ?

31 December 2019 4,410 3 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

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 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 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

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

Farrah Wahidah Ridzwan

Hello Gauri Thapa

Based on my experience, it can range from 30 mins to 24 hours.

As the site highlighted, it all depends on the current traffic and number of submissions it received.

Jamoliddin Razzokov

Gauri Thapa ATB generates a topology file for the submitted molecule. The level of accuracy of the force field parameters depends on the size of the molecule. Note that, it might generate parameters but it has to be verified first beforehand using it for specific systems. For example, there are a lot of various force field parameters that can be found for glucose in ATB but the reliable one is this (follow the link: https://atb.uq.edu.au/molecule.py?molid=461) because the solvation free energy is close to the experimental values. ATB can't generate proper force field parameters for ionic liquids (based on my previous experience).

Gauri Thapa

Thanks Farrah Wahidah Ridzwan Jamoliddin Razzokov