Dear carlos,
for example X-ca-ca-X or ca-nb-nb-ca exc ...dihedrals which include ca
(aromatic carbon) or nb (Sp2 N in pure aromatic systems) atom.. And I am
still trying to understand: for example if bond breaks at 40 degree, how
can we decide periodicity or maximum teta or exc.. Thus I am testing them
myself.
Carlos Simmerling <carlos.simmerling.gmail.com>, 4 May 2019 Cmt, 13:40
tarihinde şunu yazdı:
> What do you mean by "aromatic dihedrals"?
>
> On Sat, May 4, 2019, 5:56 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
>
> > Dear Kellon,
> > thank you so much for your help. Your assumptions are true. If I
> > understood you correctly I should do this:
> >
> > for 10,20,30 degree, I should put these values in the file respectively
> :
> >
> > r1=-360 r2=10 r3=10 r4=360
> > r1=-360 r2=10 r3=20 r4=360
> > r1=-360 r2=10 r3=30 r4=360
> > r1=-360 r2=10 r3=40 r4=360
> >
> > am I right? And my second question: Can I use these values for aromatic
> > dihedrals too? or should I change it according to what?
> > Thank you soo much again sir.
> > Best Regards,
> > Erdem
> >
> > Kellon Belfon <kellonbelfon.gmail.com>, 3 May 2019 Cum, 18:49 tarihinde
> > şunu yazdı:
> >
> > > edit: r1 = -360, r4 =360
> > >
> > > On Fri, May 3, 2019 at 11:22 AM Kellon Belfon <kellonbelfon.gmail.com>
> > > wrote:
> > >
> > > > Hi Erdem,
> > > >
> > > > I am assuming you did a 10 degree scan of your dihedral of interest
> and
> > > > you calculated the QM energies for each structure generated from your
> > > scan.
> > > >
> > > > In the next step you want to calculate the MM energy of each
> structure
> > > > without the dihedral of interest energy contribution.
> > > >
> > > > I am assuming you are using the disang file to restrain your dihedral
> > for
> > > > a minimization? If that is the case, you can keep r1 and r4 to be 360
> > > > degrees. r2=r3=dihedral_value you want to restrain. The force
> constant
> > > > seems alright.
> > > >
> > > > I am not sure what kind of structure you are fitting but remember
> after
> > > > your minimization of the QM structures, you do not want the other
> > > dihedrals
> > > > to change significantly from the dihedrals in the QM structures.
> > > >
> > > > Let me know if you have any other questions, if I am not clear or my
> > > > assumptions are incorrect.
> > > >
> > > > On Fri, May 3, 2019 at 5:37 AM Erdem Yeler <erdemyeler.gmail.com>
> > wrote:
> > > >
> > > >> Hi amberers,
> > > >> I am trying to obtain new dihedral parameters, I performed PES scan
> > > >> already. Now, I should obtain dihedral parameters with sander.I
> found
> > a
> > > >> way
> > > >> but I am not sure, so maybe you help me:
> > > >> In this tutorial:
> > > >> http://ambermd.org/tutorials/advanced/tutorial26/section2.html
> > > >> dist.example.RST file looks like this:
> > > >>
> > > >> &rst
> > > >> iat=9,99,
> > > >> r2=13,
> > > >> r2a=17,
> > > >> rk2=7.2,
> > > >>
> > > >> &end
> > > >>
> > > >> This is for bond distances according to tutorial. SO I thought and I
> > > >> decided I can use this file to calculate dihedral energy with some
> > > edits.
> > > >> Bu I am not sure how to use it dihedral. Is it okey if I use this
> file
> > > for
> > > >> example 360 degree:
> > > >>
> > > >> &rst iat= 1, 2 , 3 ,4
> > > >> r1=360.00000, r2=360.000000, r3=360.000000, r4=360.000000,
> > rk2=5000.0,
> > > >> rk3=5000.0, /
> > > >>
> > > >> and for 350 degree:
> > > >>
> > > >> &rst iat= 1, 2 , 3 ,4
> > > >> r1=350.00000, r2=350.000000, r3=350.000000, r4=350.000000,
> > rk2=5000.0,
> > > >> rk3=5000.0, /
> > > >>
> > > >> and for 340 degree
> > > >>
> > > >> &rst iat= 1, 2 , 3 ,4
> > > >> r1=340.00000, r2=340.000000, r3=340.000000, r4=340.000000,
> > rk2=5000.0,
> > > >> rk3=5000.0, /
> > > >>
> > > >> and so on......?
> > > >> I am planning to obtain MM chart for my 1-2-3-4 dihedral with this
> > way.
> > > >> (After this,I will apply Genetic Algorithm to fit amber force field
> > with
> > > >> QM
> > > >> calculation) Am I doing right?
> > > >> Thank you soo much by now.
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > > > --
> > > > Kellon A. A. Belfon, Graduate Student
> > > > Carlos Simmerling Laboratory
> > > > The Laufer Center for Physical and Quantitative Biology
> > > > The Department of Chemistry, Stony Brook University
> > > > Stony Brook, New York 11794
> > > > Phone: (347) 546-4237 <(347)+546+4237> Email:
> > kellon.belfon.stonybrook.
> > > > <kellon.belfon.stonybrook.edu>edu
> > > >
> > >
> > >
> > > --
> > > Kellon A. A. Belfon, Graduate Student
> > > Carlos Simmerling Laboratory
> > > The Laufer Center for Physical and Quantitative Biology
> > > The Department of Chemistry, Stony Brook University
> > > Stony Brook, New York 11794
> > > Phone: (347) 546-4237 <(347)+546+4237> Email:
> kellon.belfon.stonybrook.
> > > <kellon.belfon.stonybrook.edu>edu
> > > _______________________________________________
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Received on Sun May 05 2019 - 03:30:02 PDT
