From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Jul 05 2018 - 16:34:02 CDT
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
On 2018-07-05 15:22:30-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
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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