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 Sun Apr 12 2020 - 23:30:03 PDT
