[gmx-users] joining proteins at terminals

[Kit Sang Chu]

Hi everyone,

I have a macromolecular structure which contains multiple copies of
proteins. Initially, there are separate monomers and now I have to join
some of them through N/C-terminals.

However, editconf fails to recognize the merging part, possibly because
they are separated by ~ 10A. All monomers supposed to be merged are given
the same chain name in pdb. All hydrogen and terminal oxygens are stripped
out.

Are there any criteria specifically for GROMACS to recognize for merging?
Is there any specification / flag to force merging terminals?

Thanks,
Simon