[gmx-users] protein atoms with alternate conformations

[Mark Abraham]

Hi,

Swap them and see :-)

Mark

On Tue, 23 Feb 2016 20:55 Irem Altan <irem.altan at duke.edu> wrote:

> 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
>
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