[Chimera-users] Question about peptide connection

[Nicole Ostrovsky]

The modeller tool seems to be working for me, thank you very much! I will
email again if any problems arise with it.

One more question - is there a command or a tool I can use to find the
internal energy of a peptide? I have been running a 1 DS 0 CGS minimization
which means my peptide moves just slightly but I'm wondering if there is a
better way to do it.

Nicole Ostrovsky

On Mon, Jul 26, 2021 at 6:24 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Thanks, Marco -- good idea!  It might give a more reasonable result than
> manual building + minimization.
>
> Nicole, see:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative
> >
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
>
> Elaine
>
> > On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Nicole,
> >
> > you could  note the pdb name of the old structure and use the homology
> modelling tool provided in Chimera (it is based on Modeller then you need a
> password to access the server) to model the new sequence, using the old one
> as a template. Check that the alignment is correct (identical alignment
> except the new region) and let the server prepare your structure.
> >
> > Hope it helps,
> >
> > Regards,
> >
> > Marco
> >
> >
> >
> > Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
> >> Hello,
> >>
> >> I have a structure which I've cut a section out of and I am working on
> connecting the two loose ends together. I wanted to connect them with two
> glycine residues - since they are easiest to work with and have no side
> chains. I am doing this using the Modify Structure option under the Build
> structure tool and adding one atom at a time. However, when I try to
> minimize my newly created glycine, I get the error message "No MMTK name
> for atom "H1" in standard residue "GLY"" (I've attached a picture of my
> reply log). I'm not sure how to troubleshoot this.
> >>
> >> Is there a better way to connect two ends of a peptide, or should I
> change the way I am using the modify structure tool?
> >>
> >> Thank you.
> >>
> >> Nicole Ostrovsky
> >>
> >>
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> > --
> > Dr.Marco Sette, Ph.D.
> > Department of Chemical Sciences and Technology
> > University of Rome, "Tor Vergata"
> > via della Ricerca Scientifica, 00133, Rome, Italy
> > e-mail:
> > sette at uniroma2.it
> >
> > e-mail:
> > m77it at yahoo.it
> >
> > Tel.: +39-0672594424
> > Fax: +39-0672594328
> >
> > http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
> >
> >
> >
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