# Pdb2gmx handling altlocs

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-handling-altlocs/13146>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [January 26, 2026, 6:02am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-handling-altlocs/13146 "2026-01-26T06:02:09Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![prot.sim](https://avatars.discourse-cdn.com/v4/letter/p/e56c9b/32.png) [@prot.sim](https://gromacs.bioexcel.eu/u/prot.sim)\
**Post date:** [January 26, 2026, 6:02am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-handling-altlocs/13146/1 "2026-01-26T06:02:10Z")

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GROMACS version: 2025.2  
GROMACS modification: No  
How does pdb2gmx handle residues whose atoms have alternative locations? Does it pick based off of highest occupancy? What about when occupancies are equal across alternative locations?

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**Author:** ![lmullender](https://avatars.discourse-cdn.com/v4/letter/l/8dc957/32.png) [@lmullender](https://gromacs.bioexcel.eu/u/lmullender)\
**Post date:** [January 26, 2026, 9:05am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-handling-altlocs/13146/2 "2026-01-26T09:05:13Z")

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Hi! Have you tried it? I haven’t, but looking at the code it should just take the first one it finds and delete any others. It should warn you about it, though.