Generate topology file for glucose

User discussions
1

GROMACS version: 2021.4-2
GROMACS modification: No

Hello everyone!

I am fairly new to GROMACS. I’ve been able to successfully run simulations for some small molecules with the OPLS-AA force field. My problem has always been the generation of the topology files. Using pdb2gmx seems impossible for my molecules, so I have been using x2top. When x2top can’t do the work, normally because it can’t find a forcefield type for one or more atoms, I try this tool: http://erg.biophys.msu.ru/tpp/, or this tool: https://traken.chem.yale.edu/ligpargen/

So far so good. However, I am now trying to generate topology for a glucose molecule, and with x2top I get:

Generating bonds from distances…
Can not find forcefield for atom C1-2 with 3 bonds

Program: gmx x2top, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 186)

Fatal error:
Could only find a forcefield type for 23 out of 24 atoms

The tools that I’ve mentionned aren’t doing the job correctly this time. From what I could understand, the atom that x2top doesn’t seem to find is of type opls_278. Isn’t there a way to make x2top work with this information? I mean, I don’t understand why x2top doesn’t find this atom type is defined in the ffnonbonded.itp file.

I might use these files to do the job: https://atb.uq.edu.au/molecule.py?molid=22619#panel-md, but I wanted to use the OPLS-AA force field.

Thank you in advance for your answers, and I wish you all a happy new year!
Best,
Maria

2

Use CHARMM-GUI.

  1. Use Ligand modeller module to get CHARMM36 files of glucose
  2. Upload the files in the Force Field Converter module to convert to OPLS files
3

@horlust the server not providing you all the paremters for the atoms?

https://traken.chem.yale.edu/ligpargen/oplsaam_gmx_tutorial.html