Thank you sooo much Dave. I am testing right now :)
David Cerutti <dscerutti.gmail.com>, 13 Nis 2020 Pzt, 09:20 tarihinde şunu
yazdı:
> Absolutely you can use it for angle and bond scans. Enter three ambmask
> atom names for angles and specify the range in degrees. For bonds, enter
> two ambmasks and specify the range in Angstroms.
>
> Good luck,
> Dave
>
>
> On Sun, Apr 12, 2020 at 12:35 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
>
> > Dear David,
> > can we use this for scanning angles and bonds too? Thank you
> > Dear Elif,
> > I used paramfit for MM scan but when PES scan has a problem for
> > non-standart atoms, paramfit reflects this. ;For example: I obtained
> mol2
> > files from problematic PES scan. I did this because tleap's impose
> command
> > didn't run for boron atoms so I had to obtain different dihedral angles
> via
> > PES scan.. and because of the some structure are wrong I saw "a jump" in
> MM
> > scan which should not be there.
> > Erdoniko
> >
> > David Cerutti <dscerutti.gmail.com>, 11 Nis 2020 Cmt, 13:53 tarihinde
> şunu
> > yazdı:
> >
> > > The mdgx program will do what you want: see this tutorial on
> > conformational
> > > searching:
> > >
> > > http://ambermd.org/tutorials/basic/tutorial6/index.php
> > >
> > > Pretty much all you'll need is a topology, a starting coordinates file,
> > and
> > > a simple input file where you give it the atom names in ambmasks (i.e.
> > > :1.CA,
> > > or :2.OG). It will infer what type of restraint you want based on how
> > > many
> > > atoms you tell it are part of the restraint (two for bonds, three for
> > angle
> > > restraints, etc.).
> > >
> > > It can provide regular or randomized sampling over a specified
> interval.
> > > The conformation sampling feeds into force field development protocols:
> > >
> > > http://ambermd.org/tutorials/advanced/tutorial32/index.php
> > >
> > > Dave
> > >
> > >
> > > On Fri, Apr 10, 2020 at 9:31 PM Elif Çiğdem Calvin <
> > elifcigdem82.gmail.com
> > > >
> > > wrote:
> > >
> > > > Hello,
> > > > in paramfit tutuorial, dihedral angles are changing randomly with an
> > *.sh
> > > > file then single point energy calculation performes via this angles (
> > > Imean
> > > > structures).
> > > > I wonder what if I change dihedral angles regularly (for example 5
> > degree
> > > > step : 5-10-15-20 ...180 exc..) and then I calculate single point
> > > energies
> > > > and I prepare quantum_a.dat file with this data; can I obtain MM scan
> > in
> > > > the fit_output_energy.dat as (AMber +K) value? or is it wrong to use
> > this
> > > > way to calculate MM scan for a dihedral?
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Received on Mon Apr 13 2020 - 05:00:02 PDT
