How to optimize geometry of nanoparticle for docking?

Hello Folks, I want to dock nano-particle like Fe2O3 in protein. I need to optimize the geometry of such nano-particle structure. Is there any online approach to assign partial charge and...

31 December 2017 6,374 6 View

How to explain the WHATCHECK out put of SAVES Validation server?

Hello everyone,Previously, i asked a question regarding SAVES validation server (https://services.mbi.ucla.edu/SAVES/),I want to extend that question again. I could not understand why the output...

05 June 2017 5,517 0 View

How to elaborate SAVES Server output results?

04 May 2017 3,427 0 View

What's the difference between the I-TASSER and LOMETS?

Hello dear members, I want to build homology model for my target protein while using online server where the algorithm should be based on threading, because the available templates from PDB for my...

01 February 2017 1,623 2 View

Should i restraint protein and ligand in md production?

Hello folks, I want to conduct md simulation to explore the comparative stability and interaction mechanism of the reference compound (experimentally determined) and the newly screened candidate...

01 February 2017 9,253 4 View

How to ensure that whether the charge groups assigned to atoms in itp file are correct or not?

Hello, I have generated itp file for the ligand via SwissParam because I'm using CHARMm ff. I want to confirm that whether the charge groups assigned to each atom of the ligand are either correct...

10 November 2016 2,489 0 View

What's the basic criteria to select a suitable forcefield for protein-ligand complex MD simulation in gromacs?

Hello, I want to simulate my protein-lignad complex, but there is no forcefield information cited yet for this specific protein. I'm seeking the basic criteria which is taking in consideration to...

10 November 2016 933 9 View

Is there any hard and fast range for NVT and NPT to decide whether our system is equilibrated or not?

Hello, I prepared my protein-ligand complex for MD run, the average value for NVT is 299.99 which looks pretty satisfactory, but for NPT, the average value is 10.01 which is strange to me. I...

10 November 2016 2,384 7 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

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 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 Flat Lens Antenna?

28 February 2021 5,433 3 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

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 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