Re: Distorted peptide bond with new residue

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Jul 05 2018 - 19:23:06 CDT

I think you are looking for the "regenerate angles dihedrals" command,
which should be used after all patches are applied. You can avoid this by
explicitly declaring angles and dihedrals inside a residue or patch, but I
don't recommend that in general, since unexpected things can happen if you
(or someone else) calls regenerate in some other context.

Making new residues in the context of a protein/peptide is a rather
advanced task. Make sure you are correctly generating terms that cross
between residues, especially crossterms.

HTH,
BKR

On Thu, Jul 5, 2018 at 6:39 PM, Nick Palmer <tuf90798_at_temple.edu> wrote:

> I did not do that, I applied patches and generated the structure. How do
> you do that?
>
> On Thu, Jul 5, 2018, 6:05 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
> > Ahh, that's a different problem. Did you regenerate angles and dihedrals
> > after a patch? A mistake I've made more often than I'd care to admit is
> > forgetting this after a patch, and as a result not having *any* bonded
> > terms at the join point to keep the geometries sane.
> >
> > -Josh
> >
> >
> >
> > On 2018-07-05 16:00:39-06:00 Nick Palmer wrote:
> >
> > I will try the extra bonds term, however the bond is not just cis, the
> > n-co-ca bond angle is 180 degrees by the end of the minimization.
> >
> > On Thu, Jul 5, 2018, 5:34 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> > wrote:
> >
> >> Hi Nick,
> >>
> >> The initial geometry probably has more to do with it. The dihdedral that
> >> describes a peptide bond has the functional form cos(2*phi-180), which
> has
> >> minima at 0 and 180. Normally, the initial geometry is such that you get
> >> the correct trans peptide bond upon minimization, but in your case the
> >> minimizer just found the cis-peptide potential energy minimum, which
> you'll
> >> need to fix. VMD has a snazzy cis-peptide plugin (
> >> http://www.ks.uiuc.edu/Research/vmd/plugins/cispeptide/
> >> <https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fplugins%
> 2Fcispeptide%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
> 7C43be3d95ce30446d6a4d08d5e2c2bda8%7Ca0f29d7e28cd4f5484427885aee7
> c080%7C0%7C0%7C636664248394423262&sdata=qCZhFr2%2FYRVEFvufgRzcNnrhUu%
> 2BKCbQZyke1BFYk%2ByM%3D&reserved=0>)
> >> that will let you fix this for normal amino acids, although I don't
> know if
> >> the selections it uses under the hood will recognize your modified
> residue.
> >> Another possibility is to add a ridiculous extra-bonds dihedral term in
> >> addition to the regular bond to make the cis-well disappear (this is
> what
> >> the plugin sets up for you). See
> >> http://www.ks.uiuc.edu/Research/namd/2.12/ug/node27.html#
> SECTION00086400000000000000
> >> <https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.12%2Fug%2Fnode27.html%
> 23SECTION00086400000000000000&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
> 7C43be3d95ce30446d6a4d08d5e2c2bda8%7Ca0f29d7e28cd4f5484427885aee7
> c080%7C0%7C0%7C636664248394433267&sdata=8CvZWgHNPZIbSMReh0p20wOlsbtoK3
> Auay0gQjBsOBs%3D&reserved=0>
> >>
> >> -Josh
> >>
> >>
> >>
> >> On 2018-07-05 15:22:30-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
> >>
> >> Hello everyone,
> >> I have been trying to create a new residue topology and add parameters
> to
> >> it. The topology and parameters work, however when minimizing the
> structure
> >> the peptide bond connected to the c terminal of the new residue is
> >> distorted so that the peptide bond has a 0 dihedral angle rather than
> the
> >> 180 it is supposed to have. When creating the psf for this molecule, I
> had
> >> to manually link this residue to the rest of the chain with a LINK patch
>

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