Tools and information for AMBER and CPPTRAJ examples
Updated: February 9, 2024
Create a new AMBER-compatible nucleotide to perform MD simulations. In this recipe, we will use CPPTRAJ (and several other programs) to create a new nucleotide that is compatible with AMBER to run Molecular Dynamics simulations. Please notice that… Read More
Category: CPPTRAJ recipes, General
Updated: October 9, 2023
You want to measure the stacking percentage between a protein and a ligand For this recipe we will measure the stacking percentage between five ligands that have an aromatic planar component (guanine) and a protein. The system we… Read More
Category: CPPTRAJ recipes
Updated: September 30, 2023
You want to calculate how a specific change in the structure of a cyclic peptide alters the surface area. For this recipe, we are going to use three bicycle peptides that have been reported by Bennett and colaborators… Read More
Category: CPPTRAJ recipes
Updated: September 9, 2023
Incorporating a modified base (deoxy-5-methylcytosine) into DNA for MD simulation in AMBER. For this example, we are going to incorportate a modified nucleotide (5-Methylcytosine) into the DNA duplex with the sequence d(CGCGCGCGCG)2 at posiiton 3. The result will… Read More
Updated: November 1, 2022
You want to calculate the ion density around a biomolecule (protein or nucleic acid) For this recipe, we can use the Radial Distribution Function available in CPPTRAJ to calculate how the density of ions varies as a function… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General
Updated: June 2, 2022
You want to map ion density to a multidomain complex. This recipe describes how to determine grid dimensions necessary to fit part of a system, how to use the grid to calculate ion density around subunits of a… Read More
Category: CPPTRAJ recipes
Updated: June 23, 2023
You want to create a hydrogen mass repartitioned topology using CPPTRAJ In order to speed up simulations, a trick that has been used for some time is to use a redistribution of the masses of the atoms. This… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General, Topology File Commands
Updated: December 8, 2022
Reorienting small molecules to fit the orientation of another molecule You want to screen a collection of small molecules into a receptor but need to re-orient them to match a starting structure. In this recipe we will use… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General, General Concepts, Topology File Commands, Tutorials
Updated: July 31, 2020
You want to create an ensemble of PDBs from a NetCDF trajectory file. Sometimes is useful or required to extract multiple PDB files from a trajectory. In this recipe we will use the trajout command to build a… Read More
Category: CPPTRAJ, CPPTRAJ recipes, General
Updated: April 12, 2023
You want to study the hydrogen-bonds within a protein system This recipe focuses on the analysis of intra-molecular hydrogen bonds as a protein unfolds at high temperature. For an example about hydrogen bonds between two independent systems (i…. Read More
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