Dear Carlos,
thank you soo much for your answer. It really helped me.
All the Best,
Erdem
Carlos Simmerling <carlos.simmerling.gmail.com>, 5 May 2019 Paz, 13:58
tarihinde şunu yazdı:
> You can't really use a standard approach for fitting dihedrals for atoms in
> a ring. It's not possible to change 1 dihedral without either changing
> other dihedrals, or changing bonds or angles. Aromatic atoms also tend to
> have improper dihedrals as well, which further complicates the fitting. I
> would consider this a very advanced project, and in most cases you should
> just use gaff unless the relevant parameters are unavailable.
>
> On Sun, May 5, 2019, 6:04 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
>
> > 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 - 05:00:01 PDT
