# SASA Calculating for protein-ligand

**URL:** <https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [March 1, 2022, 6:46pm UTC](https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758 "2022-03-01T18:46:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![reza786](https://avatars.discourse-cdn.com/v4/letter/r/e8c25b/32.png) [@reza786](https://gromacs.bioexcel.eu/u/reza786)\
**Post date:** [March 1, 2022, 6:46pm UTC](https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758/1 "2022-03-01T18:46:24Z")

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Hi there,  
I have done my protein-ligand MD simulation and now I am going to calculate SASA for my protein-ligand complex with the spherical probe of 1.8 Å radius over the protein surface, but I have not found the right command.  
Could anyone help me?

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**Author:** ![Xabi](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/xabi/32/1206_2.png) [@Xabi](https://gromacs.bioexcel.eu/u/Xabi)\
**Post date:** [March 2, 2022, 6:51pm UTC](https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758/2 "2022-03-02T18:51:23Z")

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hey, you didn´t mention which gromacs version you are using. Anyway, the command is gmx sasa. You can have a look at the different options by typing gmx sasa -h (help). if you want to get a plot of SASA Vs simulation time for some specific residue you will have to use the -output flag and select the residue(s), atom(s) or whatever you have available inside your .ndx file.

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 3, 2022, 7:55am UTC](https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758/3 "2022-03-03T07:55:14Z")

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[https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-sasa.html](https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-sasa.html)

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**Author:** ![reza786](https://avatars.discourse-cdn.com/v4/letter/r/e8c25b/32.png) [@reza786](https://gromacs.bioexcel.eu/u/reza786)\
**Post date:** [March 3, 2022, 2:14pm UTC](https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758/4 "2022-03-03T14:14:42Z")

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Thanks for your assistance. By the way, I use GROMACS 2021.4 version.

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**Author:** ![reza786](https://avatars.discourse-cdn.com/v4/letter/r/e8c25b/32.png) [@reza786](https://gromacs.bioexcel.eu/u/reza786)\
**Post date:** [March 3, 2022, 2:15pm UTC](https://gromacs.bioexcel.eu/t/sasa-calculating-for-protein-ligand/3758/5 "2022-03-03T14:15:04Z")

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Thanks, dear.