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 - 03:00:02 PDT
