Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword]

From: Erdem Yeler <erdemyeler.gmail.com>
Date: Sat, 4 May 2019 12:57:44 +0300

Sorry, correction:

r1=-360 r2=10 r3=10 r4=360
r1=-360 r2=20 r3=20 r4=360
r1=-360 r2=30 r3=30 r4=360
r1=-360 r2=40 r3=40 r4=360

Erdem Yeler <erdemyeler.gmail.com>, 4 May 2019 Cmt, 12:56 tarihinde şunu
yazdı:

> 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:
>> >> 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
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