I want to download the amber99sb-ildn force field in gromacs to study a protein-ligand interaction using a serum protein and a TCM as a ligand, but the field cannot be seen on the gromacs tutorial page. where can I get it, @all?
Hi Larwubah Kollie,
You can use the following link to download amber99sb-ildn force field parameters.
https://gitlabph.physik.fu-berlin.de/woldeaman/gromacs/-/tree/master/share/top/amber99sb-ildn.ff?ref_type=heads
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
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
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
28 February 2021 5,433 3 View
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
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
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
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
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
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