[gmx-users] protein atoms with alternate conformations

[Irem Altan]

Hi,

I have a protein that contains atoms with alternate conformations:

ATOM    856  SG ACYS A 217       7.649  52.725  28.525  0.58 12.64           S
ATOM    859  SG BCYS A 217       7.282  54.809  26.839  0.42 15.97           S

How does pdb2gmx handle this? I checked the .gro file to see that SG ACYS was chosen (judging by the coordinates). Is it because it has a slightly higher occupancy or because it appears first?

Best,
Irem