I get this error msg during ionization stage. Any fix please?

User discussions
1

Setting the LD random seed to -759962404

Generated 102735 of the 102831 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 68640 of the 102831 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

ERROR 1 [file topol.top, line 71115]:
No such moleculetype UNK_preprocessed

There was 1 note

Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2512)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

mecky@DESKTOP-P2C3VM2:/mnt/c/vp4epi3$

2

It’s difficult to give specific help, but the problem is that there is a molecule listed in the topology (.top) file that is called UNK_preprocessed. Apparently there are no parameters loaded for that molecule type.

Did you generate the topology file using pdb2gmx? Did you get any messages indicating any problems? Are there any non-protein molecules, or non-standard residues, in the system?

3

Thank you. Yes I generated the topology file using pdb2gmx and there was no error message

4

Could you post the commands (terminal commands and interactive options) you used to generate the topology using pdb2gmx? Could you attach the topology file? You will need to rename it to, e.g., topology.txt.