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I'm trying to copy the folder "amber14sb.ff" (/home/gustavo/ComputationalChemistry/amber14sb.ff/) to the folder "top" (/usr/local/gromacs/share/gromacs/top/). I did it by using sudo cp -r /home/gustavo/ComputationalChemistry/amber14sb.ff /usr/local/gromacs/share/gromacs/top/, but the copied folder becomes not readable, and the program I'm trying to use doesn't recognize it.

How can I properly copy and paste in this system folder? Or how can I turn the copied folder readable?

Obs.: I'm on Elementary OS Loki

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    If @MichaelRoberts answer's helped you can support accepting it so it will appear as solved for other users.
    – Jorge R. Marín
    Commented Nov 11, 2016 at 16:43

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The folder permissions do not allow the application to read or write so you want to change the permissions not preserve them. After you can the folder you need to run chmod to allow it to allow read/write from no root users. You can also chown to change ownership from root to your user name. Try

sudo chmod -R 755 /home/gustavo/ComputationalChemistry/amber14sb.ff

sudo chown -R gustavo /home/gustavo/ComputationalChemistry/amber14sb.ff

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