tutorial FXR PDB numbering problem

[xy21hb]

Dear all,

I am trying to run the current version tutorial FXR, and I guess the prepared PDB has some problems with numbering, anyone has met this problem before? Many thanks for your input.

================== Command line: gmx grompp -c FXR_12-FXR_74/protein/lambda0/min01/../FullSystem.pdb -r FXR_12-FXR_74/protein/lambda0/min01/../FullSystem.pdb -f FXR_12-FXR_74/protein/lambda0/min01/min01.mdp -p FXR_12-FXR_74/protein/lambda0/min01/../SystemFull.top -o FXR_12-FXR_74/protein/lambda0/min01/min01.tpr -n FXR_12-FXR_74/protein/lambda0/min01/../index.ndx -po FXR_12-FXR_74/protein/lambda0/min01/min01_mdout.mdp -maxwarn 3

Setting the LD random seed to 1420995501 Generated 449826 of the 449826 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 449826 of the 449826 1-4 parameter combinations

ERROR 1 [file protein_step1_155527_25052023_Protein.itp, line 132]: Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 50, while at->nr = 99)

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Program: gmx grompp, version 2019.6 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1244)

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

For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors

[luancarvalhomartins]

This issue is new. Quite strange.

Would you mind sharing the protein_step1_155527_25052023_Protein.itp? Any chance it is problematic somehow?