The last module is to set up a coarse-grained simulation of a KALP peptide in its membrane environment. The second module is presenting the variation of the secondary structure which can occur for certain proteins, in our case the HIV-1 protease, and a slightly different approach (ElNeDyn) to avoid this issue. The aim of the first module of this tutorial is to define the regular work flow and protocols to set up a coarse-grained simulation of ubiquitin in a water box using a standard Martini description. Please refer to the previous tutorials (basic tutorial on Martini lipids available here) and/or the gromacs manual. In this part of the tutorial, some basic knowledge of gromacs commands is assumed and not all commands will be given explicitly. The last step can be done with the tools available in the gromacs package and/or with ad hoc scripts. However, if you want to be sure you use the same version as the files provided as an example, download this version of martinize.py. Two first steps are done using the publicly available martinize.py script, of which the latest version can be downloaded from Github. solvate the protein in the wanted environment. generating a suitable Martini topology ģ. converting an atomistic protein structure into a coarse-grained model Ģ. Setting up a coarse-grained protein simulation consists basically of three steps:ġ. Conformational changes that involve changes in the secondary structure are therefore beyond the scope of Martini coarse-grained proteins. It is noteworthy that, even though the protein is free to change its tertiary arrangement, local secondary structure is predefined and thus imposed throughout a simulation. The secondary structure of the protein influences both the selected bead types and bond/angle/dihedral parameters of each residue. Each residue has one backbone bead and zero to four side-chain beads depending on the residue type. Keeping in line with the overall Martini philosophy, the coarse-grained protein model groups 4 heavy atoms together in one coarse-grain bead. Tools and scripts used in this tutorial Soluble protein Soluble protein: the elastic network approach (if you just landed here, we recommend you follow the tutorial about lipid bilayers first) Summary
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