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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> >
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Received on Sat Apr 11 2020 - 22:00:02 PDT
