GROMACS version: 2024.1

GROMACS modification: No

Here post your question

Dear developers and users,

I converted the 5000 frame-trajectory to 250 frame-trajectory with gmx trjconv -skip. After that, I tried to run gmx trjconv -fit rot+trans command, but I got Index Error about atom numbers as you can see below. Then, I tried to make new index.ndx from npt.gro but DNA group does not seem in the index list although DNA indices have been in npt.gro. How can I fix this problem?

Command line:

**gmx_mpi trjconv -f npt_500ns_250fr.tmp.pdb -tu ns -s npt.tpr -n index.ndx -o npt_250fr.pdb -fit rot+trans**

Will write pdb: Protein data bank file

Reading file npt.tpr, VERSION 2024.1 (single precision)

Reading file npt.tpr, VERSION 2024.1 (single precision)

Group 0 ( System) has 1204488 elements

Group 1 ( Protein) has 16528 elements

Group 2 ( Protein-H) has 8194 elements

Group 3 ( C-alpha) has 1014 elements

Group 4 ( Backbone) has 3042 elements

Group 5 ( MainChain) has 4054 elements

Group 6 ( MainChain+Cb) has 5020 elements

Group 7 ( MainChain+H) has 4996 elements

Group 8 ( SideChain) has 11532 elements

Group 9 ( SideChain-H) has 4140 elements

Group 10 ( Prot-Masses) has 16528 elements

Group 11 ( non-Protein) has 1187960 elements

Group 12 ( Other) has 1754 elements

Group 13 ( ZN2) has 2 elements

Group 14 ( K) has 8 elements

Group 15 ( CLA) has 888 elements

Group 16 ( POT) has 864 elements

Group 17 ( MG) has 26 elements

Group 18 ( Ion) has 34 elements

Group 19 ( ZN2) has 2 elements

Group 20 ( K) has 8 elements

Group 21 ( CLA) has 888 elements

Group 22 ( POT) has 864 elements

Group 23 ( MG) has 26 elements

Group 24 ( DNA) has 3116 elements

Group 25 ( ZN2) has 2 elements

Group 26 ( K) has 8 elements

Group 27 ( CLA) has 888 elements

Group 28 ( POT) has 864 elements

Group 29 ( MG) has 26 elements

Group 30 ( Water) has 1183056 elements

Group 31 ( SOL) has 1183056 elements

Group 32 ( non-Water) has 21432 elements

Group 33 ( Water_and_ions) has 1183090 elements

Group 34 ( DNA_Protein) has 19644 elements

Group 35 (Water_and_ions2) has 1184844 elements

Group 36 (DNA_Protein_ZN2) has 19646 elements

Select a group: Group 0 ( System) has 1204488 elements

Group 1 ( Protein) has 16528 elements

Group 2 ( Protein-H) has 8194 elements

Group 3 ( C-alpha) has 1014 elements

Group 4 ( Backbone) has 3042 elements

Group 5 ( MainChain) has 4054 elements

Group 6 ( MainChain+Cb) has 5020 elements

Group 7 ( MainChain+H) has 4996 elements

Group 8 ( SideChain) has 11532 elements

Group 9 ( SideChain-H) has 4140 elements

Group 10 ( Prot-Masses) has 16528 elements

Group 11 ( non-Protein) has 1187960 elements

Group 12 ( Other) has 1754 elements

Group 13 ( ZN2) has 2 elements

Group 14 ( K) has 8 elements

Group 15 ( CLA) has 888 elements

Group 16 ( POT) has 864 elements

Group 17 ( MG) has 26 elements

Group 18 ( Ion) has 34 elements

Group 19 ( ZN2) has 2 elements

Group 20 ( K) has 8 elements

Group 21 ( CLA) has 888 elements

Group 22 ( POT) has 864 elements

Group 23 ( MG) has 26 elements

Group 24 ( DNA) has 3116 elements

Group 25 ( ZN2) has 2 elements

Group 26 ( K) has 8 elements

Group 27 ( CLA) has 888 elements

Group 28 ( POT) has 864 elements

Group 29 ( MG) has 26 elements

Group 30 ( Water) has 1183056 elements

Group 31 ( SOL) has 1183056 elements

Group 32 ( non-Water) has 21432 elements

Group 33 ( Water_and_ions) has 1183090 elements

Group 34 ( DNA_Protein) has 19644 elements

Group 35 (Water_and_ions2) has 1184844 elements

Group 36 (DNA_Protein_ZN2) has 19646 elements

Reading frame 0 time 0.000 b file

Precision of npt_500ns_250fr.tmp.pdb is 0.0001 (nm)

Program: gmx trjconv, version 2024.1

Source file: src/gromacs/tools/trjconv.cpp (line 1033)

Fatal error:

**Index[19638] 19647 is larger than the number of atoms in the**

**trajectory file (19646). There is a mismatch in the contents**

**of your -f, -s and/or -n files.**