[Bug-gmx_MMPBSA]: The atom 6719 in the complex index is not found in the topology file. Please check that the files are consistent.

[jjjjjqt]

Bug summary

Now there is a topology file with 6719 atoms, but gmxMMPBSA recognizes only 6718 (the 6687 atom is skipped), so that the index value cannot correspond to the topology file one by one, and finally the calculation result fails. What should I do?

Terminal output

The atom 6719 in the complex index is not found in the topology file. Please check that the files are consistent.

gmx_MMPBSA.log

[DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../peg_md_100/peg_para_md.tpr, VERSION 2022.5 (single precision) [DEBUG ] Reading file ../peg_md_100/peg_para_md.tpr, VERSION 2022.5 (single precision) [DEBUG ] Group 0 ( System) has 56744 elements [DEBUG ] Group 1 ( Other) has 1717 elements [DEBUG ] Group 2 ( MOL) has 1591 elements [DEBUG ] Group 3 ( HD1) has 17 elements [DEBUG ] Group 4 ( HD2) has 17 elements [DEBUG ] Group 5 ( HE1) has 17 elements [DEBUG ] Group 6 ( HD3) has 17 elements [DEBUG ] Group 7 ( AP1) has 12 elements [DEBUG ] Group 8 ( ZN1) has 1 elements [DEBUG ] Group 9 ( ZN2) has 1 elements [DEBUG ] Group 10 ( WT1) has 3 elements [DEBUG ] Group 11 ( WT2) has 3 elements [DEBUG ] Group 12 ( NA) has 1 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 32 elements [DEBUG ] Group 14 ( Cl-) has 6 elements [DEBUG ] Group 15 ( Protein) has 5007 elements [DEBUG ] Group 16 ( Protein-H) has 2481 elements [DEBUG ] Group 17 ( C-alpha) has 326 elements [DEBUG ] Group 18 ( Backbone) has 978 elements [DEBUG ] Group 19 ( MainChain) has 1305 elements [DEBUG ] Group 20 ( MainChain+Cb) has 1605 elements [DEBUG ] Group 21 ( MainChain+H) has 1619 elements [DEBUG ] Group 22 ( SideChain) has 3388 elements [DEBUG ] Group 23 ( SideChain-H) has 1176 elements [DEBUG ] Group 24 ( Prot-Masses) has 5007 elements [DEBUG ] Group 25 ( non-Protein) has 51737 elements [DEBUG ] Group 26 ( Ion) has 1 elements [DEBUG ] Group 27 ( Water) has 50019 elements [DEBUG ] Group 28 ( SOL) has 50019 elements [DEBUG ] Group 29 ( non-Water) has 6725 elements [DEBUG ] Group 30 ( Water_and_ions) has 50020 elements [DEBUG ] Group 31 ( protein_lig) has 5128 elements [DEBUG ] Group 32 ( rec_protein) has 5089 elements [DEBUG ] Group 33 ( envir) has 51616 elements [DEBUG ] Group 34 ( HD1) has 17 elements [DEBUG ] Group 35 ( GMXMMPBSA_REC) has 5095 elements [DEBUG ] Group 36 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 5127 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../peg_md_100/peg_md_center.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "There are only two kinds of programming languages: those people always bitch about and those nobody uses." (Bjarne Stroustrup) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 13: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [ERROR ] MMPBSA_Error

The atom 6719 in the complex index is not found in the topology file. Please check that the files are consistent.

Operating system

Linux

gmx_MMPBSA Version

No response

Python version

No response

Installation

AmberTools compilation + conda

[jjjjjqt]

@Valdes-Tresanco-MS @marioernestovaldes @BunnyRunnerX @LAndersen1

[Valdes-Tresanco-MS]

Please do not make spam mentions without an explicit need. This is bad practice. We respond in our free time, so it may take time. #477 To resolve an issue you should consider reviewing previous issues and discussions in the group. This problem has been solved several times already. Could you consider creating a new index and check if this solves the problem? Commonly, the index file does not correspond to the structure (tpr), generating a new one using this structure as a reference can solve the problem (gmx make_ndx -f md.tpr -o index.ndx) If not, please, check if the missing atom is in the topology and the complex as to supposed to be

[jjjjjqt]

Please do not make spam mentions without an explicit need. This is bad practice. We respond in our free time, so it may take time. #477 To resolve an issue you should consider reviewing previous issues and discussions in the group. This problem has been solved several times already. Could you consider creating a new index and check if this solves the problem? Commonly, the index file does not correspond to the structure (tpr), generating a new one using this structure as a reference can solve the problem (gmx make_ndx -f md.tpr -o index.ndx) If not, please, check if the missing atom is in the topology and the complex as to supposed to be

I'm very sorry if my previous mention has caused you any inconvenience. I understand that everyone is taking time out of their precious free time to help each other. I tried again to generate the index file for the tpr using 'gmx make_ndx -f', but I'm still encountering this issue. I looked for the missing atoms, and they are in the topology file. Is there any other way to solve this?

[jjjjjqt]

Thank you very much, my questions have been resolved, and I appreciate your answers.