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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat May 04 2019 - 04:00:02 PDT
