No default U-B Types

cboeckergrieme
Thu, 16 Jan 2025 03:47:01 +0000
User discussions

GROMACS version: 2024.2
GROMACS modification: No

Hello, I’m trying to simulate a lipid bilayer built by charmm-gui. When trying to create the ions.tpr file using gmx grompp and the files ions.mdp, solv.gro, and topol.top file I am creating 1520 instances of the “No default U-B Types” referencing the topol.top file. In this file, the errors are restricted to the [ angles ] section, but do not start until about 900 lines into the section.

Looking back into previous steps, I have a problem and a warning
When running this command line
!gmx_mpi pdb2gmx -f PMPE_step_5_clean.pdb -o PMPE_step_5_processed.gro -water spce -ff “charmm36_ljpme-jul2022”
I have this problem

Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
9 out of 9 lines of specbond.dat converted successfully

but it did not seem to be fatal and the step seemed to complete successfully with a 0 net charge.

When running this command line:

“!gmx_mpi solvate -cp PMPE_step_5_newbox.gro -cs spc216.gro -o PMPE_step_5_solv.gro -p PMPE_topol.top”

I get this warning:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary. Note, that this functionality may
be removed in a future GROMACS version. Please, consider
using another file format for your input.

I am pretty new to this so I do not know if these are relevant to my issue but I thought they might help.

1 post - 1 participant