Tutorial error in the "water/nvt" process (nvt_grompp.log: Fatal error: Invalid atom number 3780 in indexfile)

[Jiang-Lu-CAS]

Hi,
I failed in the "bash runall.sh" step. The protein file worked well but the water file failed in the nvt process.
Here are the details in nvt_grompp.log.

Command line:
gmx_mpi grompp -c FXR_12-FXR_74/water/lambda0/nve/nve.gro -r FXR_12-FXR_74/water/lambda0/nve/nve.gro -f FXR_12-FXR_74/water/lambda0/nvt/nvt.mdp -p FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top -o FXR_12-FXR_74/water/lambda0/nvt/nvt.tpr -n /lustre/home/jlu/software/pyautofep/t/tutorial/FXR_12-FXR_74/protein/build_system_111129_01032024/index.ndx -po FXR_12-FXR_74/water/lambda0/nvt/nvt_mdout.mdp -maxwarn 3

Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Setting the LD random seed to -885178379
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
Excluding 3 bonded neighbours molecule type 'LIG'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning H bonds into constraints...
Warning: atom name 1 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (O00_const_idx1 - O00_c)
Warning: atom name 2 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C01_const_idx2 - C01_c)
Warning: atom name 3 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (O02_const_idx3 - O02_c)
Warning: atom name 4 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C03_const_idx4 - C03_c)
Warning: atom name 5 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C04_const_idx5 - C04_c)
Warning: atom name 6 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C05_const_idx6 - C05_c)
Warning: atom name 7 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C06_const_idx7 - C06_c)
Warning: atom name 8 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C07_const_idx8 - C07_c)
Warning: atom name 9 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (N08_const_idx9 - N08_c)
Warning: atom name 10 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C09_const_idx10 - C09_c)
Warning: atom name 11 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (O0A_const_idx11 - O0A_c)
Warning: atom name 12 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C0B_const_idx12 - C0B_c)
Warning: atom name 13 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C0C_const_idx13 - C0C_c)
Warning: atom name 14 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C0D_const_idx14 - C0D_c)
Warning: atom name 15 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (N0E_const_idx15 - N0E_c)
Warning: atom name 16 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C0F_const_idx16 - C0F_c)
Warning: atom name 17 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (C0G_const_idx17 - C0G_c)
Warning: atom name 18 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (S0H_const_idx18 - S0H_c)
Warning: atom name 19 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (O0I_const_idx19 - O0I_c)
Warning: atom name 20 in FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top and FXR_12-FXR_74/water/lambda0/nve/nve.gro does not match (O0J_const_idx20 - O0J_c)
(more than 20 non-matching atom names)

WARNING 1 [file fullsystem_111141_01032024.top, line 55]:
58 non-matching atom names
atom names from
FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top will be
used
atom names from FXR_12-FXR_74/water/lambda0/nve/nve.gro will be ignored

Cleaning up constraints and constant bonded interactions with virtual sites
Removing all charge groups because cutoff-scheme=Verlet

---

Program: gmx grompp, version 2019.3
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2661)

Fatal error:
Invalid atom number 3780 in indexfile

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

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

After check, I found it's due to the wrong index file （protein/..)

gmx_mpi grompp -c FXR_12-FXR_74/water/lambda0/nve/nve.gro -r FXR_12-FXR_74/water/lambda0/nve/nve.gro -f FXR_12-FXR_74/water/lambda0/nvt/nvt.mdp -p FXR_12-FXR_74/water/lambda0/nvt/../fullsystem_111141_01032024.top -o FXR_12-FXR_74/water/lambda0/nvt/nvt.tpr -n /lustre/home/jlu/software/pyautofep/t/tutorial/FXR_12-FXR_74/### protein/build_system_111129_01032024/index.ndx -po FXR_12-FXR_74/water/lambda0/nvt/nvt_mdout.mdp -maxwarn 3

Can you help us solve this problem. Thanks.

Jiang

[YumizSui]

I encountered the same problem.
It seems that the implementation of the path to the index file provided for the water system in prepare_dual_topology.py is incorrect.
For example, in runall_FXR_12-FXR_74_water.sh, tutorial/FXR_12-FXR_74/protein/build_system_*/index.ndx is specified, but this should actually specify tutorial/FXR_12-FXR_74/water/build_water_*/index.ndx.

[Jiang-Lu-CAS]

I encountered the same problem. It seems that the implementation of the path to the index file provided for the water system in prepare_dual_topology.py is incorrect. For example, in runall_FXR_12-FXR_74_water.sh, tutorial/FXR_12-FXR_74/protein/build_system_*/index.ndx is specified, but this should actually specify tutorial/FXR_12-FXR_74/water/build_water_*/index.ndx.

@YumizSui Yes, I corrected it by hand and it worked after I replace the protein index to the right water index. Unfortunately, it failed again in the analysis step, which looked like the water file missed several code compared with the protein run file. The author should correct the code. Have you run it completely? How did you solve the problems? Thanks.

[TIAN298]

Hello, I encountered with same problems, and I think it is related with command lines from "tutorial/FXR_12-FXR_74/runall_FXR_12-FXR_74_water.sh" , which is generated from prepare_dual_topology.py. But I still cannot get it right, I wonder have you guys solved this problem?