# Protein-Ligand Complex Analysis FIRST FRAME EXTRACTION

**URL:** <https://gromacs.bioexcel.eu/t/protein-ligand-complex-analysis-first-frame-extraction/953>\
**Category:** User discussions\
**Created:** [October 13, 2020, 10:27am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-analysis-first-frame-extraction/953 "2020-10-13T10:27:31Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mjsubach](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjsubach/32/387_2.png) [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\
**Post date:** [October 13, 2020, 10:27am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-analysis-first-frame-extraction/953/1 "2020-10-13T10:27:31Z")

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GROMACS version: 2020.3  
GROMACS modification: Yes/No  
Here post your question:

Hello for the above topic my understanding is that via the commands:

gmx trjconv -s md\_0\_10.tpr -f md\_0\_10.xtc -o md\_0\_10\_center.xtc -center -pbc mol -ur compact

gmx trjconv -s md\_0\_10.tpr -f md\_0\_10\_center.xtc -o start.pdb -dump 0

my output start.pdb should contain the ligand, solvent and ion coordinates to match the tutorials exhibited below visualization via VMD, however, my output start.pdb only contains protein coordinates (my md\_0\_10.gro contains protein-ligand-sol-ion coordinates). Any clarification would be helpful:)

Thanks:)  
Joel

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**Author:** ![lindahl](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/lindahl/32/415_2.png) [@lindahl](https://gromacs.bioexcel.eu/u/lindahl)\
**Post date:** [October 13, 2020, 12:11pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-analysis-first-frame-extraction/953/2 "2020-10-13T12:11:25Z")

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I can only imagine two places where you might have gotten rid of the water (if you double-checked the end of start.pdb in the terminal to make really sure it didn’t contain the lines for water):

1. You might have chosen to only write the protein to the compressed trajectory by using the xtc-grps option in the mdp file.

2. You selected “1” for the interactive option when asked (at either invocation) by gmx trjconv about what group to write to the output.

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [October 13, 2020, 12:13pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-analysis-first-frame-extraction/953/3 "2020-10-13T12:13:12Z")

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You might have `.mdp` output settings to only give you the protein coordinates in output to save disk space. Changing  
[compressed-x-grps](http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-compressed-x-grps) will change that to give you more output on the trajectory.

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**Author:** ![mjsubach](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjsubach/32/387_2.png) [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\
**Post date:** [October 13, 2020, 1:57pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-analysis-first-frame-extraction/953/4 "2020-10-13T13:57:35Z")

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Hello Sir Lindhal and thank you for your kind update, yes I carelessly selected 1 initially for the later command out of habit via the former command selection.

Best,  
Joel