Create new project: provide structure - BioExcel Building Blocks Workflows

Create project from structure

In this category users can custom, configure and execute the following workflows related with MD setup of structures. Take into account that the availability of each project depends on the structure checking parameters and the inputs provided:

GROMACS Set Up GROMACS Complex Set Up AMBER Set Up AMBER Complex Set Up GROMACS Set Up Mutations

Provide
structure

Check
structure

Settings

Run
project

provide structure

Please, select a single PDB file from your computer. Input structure file should follow PDB File Format v.3.30 (July 13, 2011), click here for more info.

Note that, in order to avoid future problems in the workflow, all the hydrogens present in the structure will be removed. Heteroatoms present in structure, must be tagged as HETATM instead of ATOM in order for the server to properly recognize them.

Upload a structure from its corresponding PDB ID.

Insert here the PDB ID

Select assembly

Upload an AlphaFold structure from its corresponding Uniprot ID.

Perform a search on the Protein Data Bank.