[gmx-users] joining proteins at terminals

paul buscemi pbuscemi at q.com
Wed Oct 10 12:48:24 CEST 2018

Try giving residues in the macro-macro structure the same name … or possibly get rid of the 10A gap by using additional amino acids like gly-gly gly ?

> On Oct 9, 2018, at 5:28 PM, Kit Sang Chu <kschu at ucdavis.edu> wrote:
> 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
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