GROMACS Polysaccharide Simulation Tutorial

In the past, it was not easy to use MD to simulate sugar molecules, because the force fields designed for proteins and nucleic acids are not suitable for sugar molecules, so it is necessary to modify the commonly used force fields. You can refer to the following reference:

  • CHARMM: Carbohydrate Solution Simulations: Producing A Force Field With Experimentally Consistent Primary Alcohol Rotational Frequencies And Populations. Michelle Kuttel, J. W. Brady, Kevin J. Naidoo; J. Comput. Chem. 2002.23(13):1236-1243.
  • OPLSAA: An Improved Opls-aa Force Field For Carbohydrates. D. Kony, W. Damm, S. Stoll, W. F. Van Gunsteren; J. Comput. Chem.2002, 23(15):1416-1429.
  • GROMOS: A New Gromos Force Field For Hexopyranose-based Carbohydrates. Roberto D. Lins, Philippe H. Hünenberger; J. Comput. Chem. 2002, 26(13):1400-1412.

Tutorial

At present, the most widely used polysaccharide force field is GLYCAM:

GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

Here is a simple example of how to use AmberTools and acpype to create a GROMACS input file of polysaccharides and simulate.

Procedures

AmberTools: Used to generate AMBER input files. You can download, compile and install the official version.

acpype script: used to convert AMBER input files into GROMACS input files.

Step1: Generate AMBER input file

Use the examples in the manual to familiarize yourself with the construction methods of polysaccharides.
Create a file gly
sourceleaprc.GLYCAM_06
gly=sequence{ROH4YB4YB3MB0MA}
psi imposegly{32}{{C1O4C4H40.0}} imposegly{43}{{C1O4C4H40.0}}
saveamberparmglygly.topgly.crd savepdbglygly.pdb savemol2glygly.mol2
quit

It is recommended to save the configuration in both the pdb format and the mol2 format. Compared with the pdb format, the mol2 format saves more information related to the force field, such as atom type, electric charge, etc. It is more convenient to view and modify, and it can also be used directly AmberTools processing.

Use the sleap command to generate AMBER input files
sleap -f gly.in
In this way, we get the Amber input file of polysaccharide: topology gly.top, coordinate gly.crd, configuration gly.mol2.

Step 2: Convert to GROMACS input file

Use acpype to convert AMBER input files to GROMACS input files
acpype -p gly.top -x gly.crd -d

You will get the GROMACS coordinate file gly_GMX.gro and the topology file gly_GMX.top. In addition, acpype will automatically give two mdp files: em.mdp and md.mdp, but they are basically useless, because there are too few settings.

Step 3: Run GROMACS simulation

After getting the coordinate file and topology file, prepare the mdp file and index file, and follow the usual process to simulate.

Since GLYCAM and AMBER force fields belong to the same series, TIP3P is recommended for water models.

Notes

For a system that uses both AMBER and GLYCAM force fields, how to set the correction factor of 1-4 non-key action? The easiest way is to use the AMBER force field settings 0.5 and 0.8333 directly. In this way, the accuracy of GLYCAM will be lowered, but if you are more concerned about the configuration of the protein, this method is not impossible. In fact, both Amber and GROMACS can achieve the use of mixed 1-4 non-bonding factors. In GROMACS, just put the [pairs] part Change the function type to 2, and provide five parameters: fudgeQQ, q_i, q_j, sigma_ij, epsilon_ij.

* It should be noted that our service is only used for research, not for clinical use.

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