# Erro with index file **URL:** \ **Category:** User discussions\ **Created:** [January 16, 2021, 4:27pm UTC](https://gromacs.bioexcel.eu/t/erro-with-index-file/1447 "2021-01-16T16:27:03Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [January 16, 2021, 4:27pm UTC](https://gromacs.bioexcel.eu/t/erro-with-index-file/1447/1 "2021-01-16T16:27:03Z")
GROMACS version:2020.4 GROMACS modification: No Here post your question: GROMACS: gmx distance, version 2020.4 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /ricardo2/ricardo/lab\_alunos/veronica/tipi\_files/gromacs\_files/tipi-wt\_HNE/tutorial\_umbrella Command line: gmx distance -s tipi-wt\_HNE\_pullc.tpr -f tipi-wt\_HNE\_pull\_conf0.gro -select ‘com of group “Chain\_E” plus com of group “Chain\_I”’ -n index.ndx -oall tipi-wt\_HNE\_dist0.xvg Reading file tipi-wt\_HNE\_pullc.tpr, VERSION 2020.4 (single precision) Reading file tipi-wt\_HNE\_pullc.tpr, VERSION 2020.4 (single precision) * * * Program: gmx distance, version 2020.4 Source file: src/gromacs/selection/selectioncollection.cpp (line 614) Function: void gmx::SelectionCollection::setTopology(gmx\_mtop\_t\*, int) Inconsistency in user input: Invalid index group references encountered Group ‘Chain\_E’ cannot be used in selections, because it contains negative atom indices and/or references atoms not present (largest allowed atom index is 1010). Group ‘Chain\_I’ cannot be used in selections, because it contains negative atom indices and/or references atoms not present (largest allowed atom index is 1010). ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [January 18, 2021, 5:15pm UTC](https://gromacs.bioexcel.eu/t/erro-with-index-file/1447/2 "2021-01-18T17:15:41Z")
Hi, it looks like that index file and gro file are not compatible. You can re-generate the index file using gmx make\_ndx and giving as input the gro tipi-wt\_HNE\_pull\_conf0.gro. Best regards Alessandra ---
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [January 20, 2021, 12:49am UTC](https://gromacs.bioexcel.eu/t/erro-with-index-file/1447/3 "2021-01-20T00:49:31Z")
Hi, Alessandra. Thanks for your help, but I loose this works and start another but now I’m not able to reproduce the last one. Now I have the follow problem: Command line: gmx grompp -f md\_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘optimize\_fft’ Ignoring obsolete mdp entry ‘ns\_type’ Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’ Setting the LD random seed to 1461744737 Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_E’ turning H bonds into constraints… Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_I’ 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… Excluding 1 bonded neighbours molecule type ‘CL’ turning H bonds into constraints… WARNING 1 [file topol.top, line 50]: The following macros were defined in the ‘define’ mdp field with the -D prefix, but were not used in the topology: POSRES\_B If you haven’t made a spelling error, either use the macro you defined, or don’t define the macro Pull group 1 ‘Chain\_E’ has 3565 atoms Pull group 2 ‘Chain\_I’ has 860 atoms Number of degrees of freedom in T-Coupling group Protein is 9552.59 Number of degrees of freedom in T-Coupling group non-Protein is 60159.41 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.493 nm, buffer size 0.093 nm Set rlist, assuming 4x4 atom pair-list, to 1.418 nm, buffer size 0.018 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 100.000 Using frame at t = 100 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x40x100, spacing 0.117 0.109 0.120 Pull group natoms pbc atom distance at start reference at t=0 1 3565 1783 2 860 3389 0.218 nm 0.218 nm Estimate for the relative computational load of the PME mesh part: 0.13 This run will generate roughly 319 Mb of data There was 1 warning * * * Program: gmx grompp, version 2020.4 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option Please, can you help again thanks in advance Ricardo ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [January 22, 2021, 1:20pm UTC](https://gromacs.bioexcel.eu/t/erro-with-index-file/1447/4 "2021-01-22T13:20:02Z")
Hi, The 'define" option in mdp does not match with the provided input files. Look what is associated to the option ‘define’ in your mdp file and check that definition is also giving in the topology file more define option in [Molecular dynamics parameters (.mdp options) — GROMACS 2020.5 documentation](https://manual.gromacs.org/current/user-guide/mdp-options.html) In general, it is good praxis to create a new topic for each new problem or questions, such as the title match with the problem and facilitate the answer of other users. Best regards Alessandra