ERROR 164 [file topol.top, line 100195]: No default Ryckaert-Bell. types

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GROMACS version: 2020.1
GROMACS modification: No

Hi all,

I am trying to simulate a system with triethyl citrate molecule. Initially I built the molecule by mapping the atoms to the opls_aa atom types. I modified the rtp file by including the atom names, types, and charges. Also defined the bonds accordingly.

I, then, generated the topology of the system (with 400 molecules) using ‘pdb2gmx’. In the .top file, I can see that angles and dihedrals section got fulfilled automatically with specific function name. But the function constants are absent.

When I used ‘grompp’ to generate the ‘.tpr’ for energy minimization I got around 400 errors “No default Ryckaert-Bell. types”.

Can some one please let me know how to overcome this error?

Thanks in advance.

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In general, gmx pdb2gmx are not meant to generate topologies for small molecules, but rather for proteins, RNA, DNA etc.

Use other programs instead, such as acpype, antechamber, CGenFF (via web interface), STaGE or even gmx x2top. See Running membrane simulations in GROMACS - GROMACS 2024.4 documentation and System preparation - GROMACS 2024.4 documentation for some more information.

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Thanks for your reply, Magnus.
I am new to topology creation in GROMACS. Can you please help me with the following? I searched the available information, but could not clearly get hold of it.

  1. For a specific molecule (non-protein) what is the usual flow for topology generation? When should I turn to DFT for forcefield parametrization?
  2. How exactly should x2top be used for this specific molecule (non-protein)?

Having asked that. This is what I have done till now.

  1. I started with pdb2gmx, where I built the atoms and bonds in rtp file. Then when I ran pdb2gmx with the pdb file, I was getting the topol file. But, when I was generating the tpr, I was getting “No default Ryckaert-Bell types” error.
  2. Then I changed to using x2top (after gping through the documentation). I built a pdb file for my molecule. Assigned different atom names in the pdb file.
  3. Used this command “gmx_mpi x2top -f TEC_atb.pdb -o topol.top -name TEC -param yes -ff select” to generate topology. Selected various ff, like oplsaa, and charmms36.
  4. In oplsaa case, i am getting an error that only 32 out of 39 atoms were detected. In case of charmms36, “atomname2type.n2t file is missing” was the error.
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I’ve honestly never used gmx x2top and it’s quite primitive as far as I’ve understood. I think the other alternatives I listed may be easier to use.