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.
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>
--
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 Fri May 03 2019 - 08:30:04 PDT
