From the looks of it, you do not have the right ambmasks for your atoms.
There is only one residue in the topology, called "RES." The atoms you want
in it are :1.O1 :1.B1 :1.O1D :1.C1D (or go for the B branch instead). The
(:) means "residue" and @ "atom" in ambmask syntax. I confess I didn't
anticipate this use case, so the error message is a little misleading when
it does not find any atoms. But, this is an ambmask syntax issue, not a
familiarity with mdgx issue yet. From what it appears you are trying to
do, you are catching along fine.
Dave
On Wed, Apr 15, 2020 at 5:26 PM Erdem Yeler <erdemyeler.gmail.com> wrote:
>
> Dear David,
> I tried to run here is my input file:
> &files
>  -p  x.prmtop
>  -c  x.inpcrd
>  -o  x.out
> &end
> &configs
> Â % Backbone phi and psi sampling
>   GridSample :7.O :1.B :6.O :8.C { -180.0 180.0 } fbhwÂ
> 10.0Â Krst 64.0,
> Â % General minimization instructions
> Â count = 64,
> Â verbose 1,
> Â maxcyc = 5000,
> Â strainlim = 20.0,
> Â bstrain = 10.0,
> Â astrain = 10.0,
> Â % Reshuffling conformations to best achieve each minimum
> Â nshuffle = 2,
> Â shuffle bootstrap,
> Â % Output controls
> Â outbase 'Conf', 'Conf',
>  write  'cdf', 'pdb',
>  outsuff 'cdf', 'pdb',
> &end
> and I attached my prmtop and crd files.
> But I got this error:
> SeekManipulator >> Error. Manipulator command contains too many atom
> names:
> Â ridSample :7.O :1.B :6.O :8.C { -180.0 180.0 } fbhw 10.0 Krst 64.0
> I am very new using mdgx. Could you help me? Where is my mistake?
> I want to scan O-B-O-C dihedral from -180 to 180
> Thank you.
> image.png
>
> Erdem Yeler <[1]erdemyeler.gmail.com>, 13 Nis 2020 Pzt, 14:37
> tarihinde Åunu
> yazdı:
>
> Thank you sooo much Dave. I am testing right now :)
>
> David Cerutti <[2]dscerutti.gmail.com>, 13 Nis 2020 Pzt, 09:20
> tarihinde
> Åunu 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 <[3]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 <[4]dscerutti.gmail.com>, 11 Nis 2020 Cmt, 13:53
> tarihinde
> Åunu
> > yazdı:
> >
> > > The mdgx program will do what you want: see this tutorial on
> > conformational
> > > searching:
> > >
> > > [5]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:
> > >
> > > [6]http://ambermd.org/tutorials/advanced/tutorial32/index.php
> > >
> > > Dave
> > >
> > >
> > > On Fri, Apr 10, 2020 at 9:31 PM Elif ÃiÄdem Calvin <
> > [7]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?
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > [8]AMBER.ambermd.org
> > > > [9]http://lists.ambermd.org/mailman/listinfo/amber
> > > >
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> > > AMBER mailing list
> > > [10]AMBER.ambermd.org
> > > [11]http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> >
> _______________________________________________
> AMBER mailing list
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>
> References
>
> 1. mailto:erdemyeler.gmail.com
> 2. mailto:dscerutti.gmail.com
> 3. mailto:erdemyeler.gmail.com
> 4. mailto:dscerutti.gmail.com
> 5. http://ambermd.org/tutorials/basic/tutorial6/index.php
> 6. http://ambermd.org/tutorials/advanced/tutorial32/index.php
> 7. mailto:elifcigdem82.gmail.com
> 8. mailto:AMBER.ambermd.org
> 9. http://lists.ambermd.org/mailman/listinfo/amber
> 10. mailto:AMBER.ambermd.org
> 11. http://lists.ambermd.org/mailman/listinfo/amber
> 12. mailto:AMBER.ambermd.org
> 13. http://lists.ambermd.org/mailman/listinfo/amber
> 14. mailto:AMBER.ambermd.org
> 15. http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 15 2020 - 15:00:02 PDT
