[gmx-users] joining proteins at terminals

[Kit Sang Chu]

Hi Paul,

Giving the same name you mean same "chain name"? I tried but the problem
persists. For my specific case I cannot add extra amino acids. I just have
to minimize the energy to pull them closer.

Regards,
Simon Kit Sang Chu
Ph.D. student
Biophysics Graduate Group
University of California Davis


On Wed, Oct 10, 2018 at 3:48 AM paul buscemi <pbuscemi at q.com> wrote:

> 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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