I used these instructions:

gmx trjconv -f step5_1.xtc -s step5_1.tpr -b 0 -e 2 -o firstframe.gro

gmx trjconv -f step5_1.xtc -s firstframe.gro -pbc nojump -o traj2-pbc.xtc -dt 10

gmx trjconv -pbc atom -ur compact -s step5_1.tpr -f traj2-pbc.xtc -n index2.ndx -o step5_1_compact.xtc

gmx trjconv -f step5_1_compact.xtc -s firstframe.gro -fit rot+trans -o step5_1_noPBC_ok.xtc

In the last instruction show this:

WARNING: Masses and atomic (Van der Waals) radii will be guessed

based on residue and atom names, since they could not be

definitively assigned from the information in your input

files. These guessed numbers might deviate from the mass

and radius of the atom type. Please check the output

files if necessary.

Can not find mass in database for atom ZN in residue 56 ZN2

Can not find mass in database for atom ZN in residue 57 ZN2

-------------------------------------------------------

Program: gmx trjconv, version 2019.6

Source file: src/gromacs/fileio/confio.cpp (line 517)

Fatal error:

Masses were requested, but for some atom(s) masses could not be found in the

database. Use a tpr file as input, if possible, or add these atoms to the mass

database.

How I can Use a tpr file as input? or Add these atoms to the mass database of GROMACS 2019.6?

Hi,

There is no need to extract firstframe.gro and use it (To extract one frame use -dump option); Instead use md.tpr in every command.

You can also try using pbc -mol -ur compact in one command.

Hej!

Sumedha Bhosale, that is what I excatly usually use with VMD.

Akiko Mendoza, I have never tried with Chimera but you can try these commands, which solved my same issue with VMD.

trjconv -f *.xtc -s *.tpr -pbc nojump #tjumps will be removed

trjconv -f *.xtc -s *.tpr -pbc mol -ur compact -center #put everything in the box

or try to check help with trjconv -h, documentation;

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Thank you Hüsamettin,

Only, I have doubt about using -ur compact and -center at the same time:

-ur compact: puts all atoms at the closest distance from the center of the box

-center : centers the system in the box.

Hi Akiko,

You do not need to use both since -center works the same in a way. Just give it a try these commands and let us know if you still are having a problem.

/Hüsamettin

Akiko Mendoza use VMD and your problem will be solved.

VMD is more specific with MD trajectories analysis.

best regards.

Thank you Hüsamettin,

At this moment at tried these instructions to fix only protein-RNA and works excellent, no jumps, only one position for both molecules.

.-Make index

gmx make_ndx -f step5_1.gro -o index.ndx

gmx make_ndx -f step5_1.gro -n index.ndx -o index.ndx

1.-No jumps

gmx trjconv -f step5_1.xtc -s step5_1.tpr -n index.ndx -b 0 -e 2 -o firstframe.gro

output system

gmx trjconv -f step5_1.xtc -s firstframe.gro -n index.ndx -pbc nojump -o traj2-pbc.xtc -dt 10

output system

2.-Center system

gmx trjconv -pbc mol -center -s step5_1.tpr -f traj2-pbc.xtc -n index.ndx -o step5_1_center.xtc

select: protein-rna/output: protein-rna

3.-file.tpr only for Protein-RNA

gmx convert-tpr -s step5_1.tpr -n index.ndx -o NC-RNA.tpr

select: Protein-RNA

4.-Fix molecules

gmx trjconv -f step5_1_center.xtc -s NC-RNA.tpr -n index.ndx -fit rot+trans -o step5_1_noPBC_fit.xtc

select: Protein-RNA/ output group Protein_RNA