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.
>> _______________________________________________
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>> 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 Fri May 03 2019 - 09:00:02 PDT
