Re: Distorted peptide bond with new residue

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Thu Jul 05 2018 - 17:00:25 CDT

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/) 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
>
> -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.
> Could the link patch change the type of the bond somehow?
> Thank you in advance
> --
> Nicholas J. Palmer
>
>

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