[gmx-users] Protein Chains Spatially Separated After Energy Minimization

[Benjamin Er]

Hello Everybody,

I have 2 different protein chains (not a homodimer), chain C and chain F in
a PDB file.
These 2 proteins are interacting proteins close in proximity.
I would like to use energy minimization (EM) and equilibration (EQ) to
approximate the most relaxed interacting conformation between these 2
proteins.
However, after EM, these 2 chains become far apart in space. (I checked
with PyMOL using editconf for the resulting EM .gro file)
My previous EM and EQ run for a different set of 2 proteins did not have
this error.
May I please know how I can rectify this?

Thank you!
- Benjamin
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