[gmx-users] joining proteins at terminals

[Kit Sang Chu]

Thanks, Justin. For the current state, it is still exploratory so I will
try to avoid adding extra residues as linkers. Yes, I meant pdb2gmx. Sorry
for the confusion.

You mention I can feed in a .rtp file as an entry. How should I do that
specifically?

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


On Wed, Oct 10, 2018 at 2:59 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/10/18 5:57 PM, Kit Sang Chu wrote:
> > Hi everyone,
> >
> > In general, what is the GROMACS's criteria to bond terminals? I should
> > check whether I have met all of them. Perhaps I miss one or two.
>
> I don't follow what you're trying to do. editconf doesn't make bonds.
> pdb2gmx does, but it only links what you tell it. You can tell pdb2gmx
> to bond anything at any distance with an .rtp entry, but you'll get a
> long bond warning and your system may not minimize if the C-N distance
> is indeed 10 A.
>
> -Justin
>
> > Regards,
> > Simon Kit Sang Chu
> > Ph.D. student
> > Biophysics Graduate Group
> > University of California Davis
> >
> >
> > On Wed, Oct 10, 2018 at 11:22 AM Kit Sang Chu <kschu at ucdavis.edu> wrote:
> >
> >> 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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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