To the list with the overly large images removed so that it actually makes it...
On Fri, Jul 12, 2019 at 4:20 PM Greg Landrum <greg.land...@gmail.com> wrote: > Hi > > I can't reproduce what you say you're seeing. Here's my example: > > https://nbviewer.jupyter.org/gist/greglandrum/fd828137e337a6d06c9cc275b7215ba1 > > What do you get if you try that bit of code? > > -greg > > > On Wed, Jul 10, 2019 at 6:40 PM Phuong Chau <pc...@smith.edu> wrote: > >> Dear all, >> I have tried changing one of my torsion to (2,1,0,5) but I still have the >> same problem with the pdb structure file: C -C -C -C =C . The last three C >> is still having a 180 degree angle instead of 120 degree. However, if I >> delete completely the torsion (2,1,0,5), it gave me the all-Trans structure >> as the following: >> >> >> >> Additionally, I have tried to the same script with CCC=C, CCCC=O, CCCCC=C >> and CCCCCC=C, it all gave me the all-Trans structrures that I want. Do you >> know if I should change the forcefield? I am not sure why the weird >> structure only happened with the torsions of CCCC=C. >> >> Thank you so much for your help. >> >> Best regards, >> Phuong Chau >> Smith College '20 >> Engineering and Data Science Major >> >> >> On Tue, Jul 9, 2019 at 9:49 PM Greg Landrum <greg.land...@gmail.com> >> wrote: >> >>> Hi, >>> >>> It looks like the atom ordering in one of your torsions is wrong. Try >>> changing (2, 0, 1, 5) to (2, 1, 0, 5) and that should clear things up. The >>> ordering of the atoms in the constraints is important. >>> >>> -greg >>> >>> >>>>
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