MD: cyclopeptides setup

Introduction

How setup a MD simulation for a cyclopeptide

The cyclopeptide has to be built following particular protocol to be sure that it is considered as a cyclopeptide in GROMACS and in other software.

How build the  cyclopeptide

Build of the cyclopeptide using Vega

Open Vega

• If the installation is required, the link to the software is https://nova.disfarm.unimi.it/cms/index.php

Open the peptide builder Modify - Build - Peptide

Write the sequence in the windows using the one-letter code for the amino acids

Click on the Add lateral chains option and choose alpha helix structure

Finally, click on the build button

Now, use Modify - Remove - Atom to delete two hydrogen atoms on the N-terminus and the hydrogen on the C-terminus

Then, use Modify - Add - Bonds and connect the N-terminus with the C- terminus

Calculate - Charge & Potential end select GAFF_SMARTS as Force Field and Ammp-Mom as charges

• It should be work but other charges can be used because here we want to prepare a starting structure to submit to GROMACS that will recalculate charges

Calculate - Ammp - Minimization

Firstly, use default parameter and Truncated-Newton to minimize the structure, if necessary repeat this step

Calculate - Ramachandran Plot

If the cyclopeptide shows a good distribution in the Ramachandran plot then the structure is ok otherwise try to minimize with the genetic algorithm

To obtain other starting structure, it is possible to use the conformational analysis tool

Calculate - Ammp - Conformational search

• In the windows click on Modify torsions
• In the new window Modify - Add proteic torsions - Phi and Psi and then close the window
• Run the conformational search using all default parameters and Boltzmann jump or Random method
• Minimize structure and check the Ramachandran plot

When at least one satisfactory model is obtained, it is possible to use the model as starting point for the next steps

• It should be useful to obtain more than one model
• WARNING: hydrogen atomes bound to the backbone amidic nitrogen shoutl be named H without numbers. It could happen that in the first or in the last amino acid there is a number in the name that must be deleted (e.g. H1 must be modified in H without changes in the file format) .

Prepare cyclopeptide in GROMACS

We follow the instruction in https://github.com/visvaldask/gmx_makecyclictop using the Perl script downloadable in the same github site

First step, take your cyclic peptide/nucleotide pdb file and imagine it�s linear (for a moment).

Add using text editor additional 2 additional residues to N and C termini.

The additional residues should be as follows. The one added in the beginning should be taken from the end, and the one added to the end should be taken from the beginning.

• Delete the bond section of the pdb file

Next step is renumbering residues (by hand) - important. Renumber first and last residues by hand so that they follow one after another; the first will be 0, and the last will be N+1, where N is the number of the amino acids in the cyclic peptide.

The atom numbering is in a mess but it�s not important, just the residue numbers are important.

Next run your edited file (let's say myfile.pdb) through GROMACS using command something like:

GROMACS creates topology file, write down it�s name (probably topol.top, but could be something else, like .itp file; if .itp is created, you should use it instead of .top for step 3)

Now run the perl script on that top file:

where topfile is the topology file created in step (2)

The script creates new topology file, e.g. topol_cyc.top.

Now we just have to make sure we have the PDB (or GRO) file matching it.

For this, delete the residues added at step (1) from the GROMACS generated file (myfile_gmx.pdb)

Let's say the edited myfile_gmx.pdb without the first and last residues is named myfile_gmx_edit.pdb

Use that file for your simulation purposes, e.g. convert it to GRO and add simulation box:

Use myfile_gmx_edit.gro and topol_cyc.top for futher GROMACS simulations.

Summary of the instructions for MD preparation

Preparation mv1_model1_gmx.pdb from mv1_model1.pdb by repetition of two residues (the last as first residue and the first as last)

gmx pdb2gmx -f mv1_model1_temp.pdb -o mv1_model1_gmx.pdb

./gmx_makecyclictop.pl topol.top

Edit mv1_model1_gmx.pdb and delete the first and the last residue and save it (e.g. mv1_model1_edit.pdb)

gmx editconf -f mv1_model1_edit.pdb -o mv1_model1_edit.gro -c -d 1.0 -bt cubic

gmx solvate -cp mv1_model1_edit.gro -cs spc216.gro -o mv1_model1_solv.gro -p topol_cyc.top

gmx grompp -f minim.mdp -c mv1_model1_solv.gro -p topol_cyc.top -o em

gmx mdrun -v -deffnm em

Appendix

File minim.mdp