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From: Erdem Yeler <erdemyeler.gmail.com>

Date: Sat, 4 May 2019 12:56:05 +0300

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

Date: Sat, 4 May 2019 12:56:05 +0300

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:

_______________________________________________

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Received on Sat May 04 2019 - 03:00:02 PDT

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