[gmx-users] joining proteins at terminals

[Kit Sang Chu]

Thank you, Justin.

After some more work, I finally get it done. The problem is the ordering of
chains in pdb. All joined chains must be printed consecutively, in the
order of N to C-terminal. Resid does not play a role.

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


On Wed, Oct 10, 2018 at 4:33 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/11/18 2:21 AM, Kit Sang Chu wrote:
> > 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?
>
> There's nothing really to do. You concatenate the coordinates of the
> proteins, give them the same chain identifier (or ensure there are no
> TER cards between them) and run pdb2gmx. It should process it as a
> single protein.
>
> -Justin
>
> > 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
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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