Yes, QMMM is only available in Sander.
Feng
On Mon, Apr 17, 2017 at 12:50 PM, Samaneh Ghassabi Kondalaji <
saghassabikondalaji.mix.wvu.edu> wrote:
> Update after fixing all errors:
> As it turns out, I had fixed the update 4 and 9 errors before! The
> $AMBERHOME/update_amber --show-unapplied-patches does not return any value
> for unapplied patches. I don't remember exactly but I assume the error was
> gone after I solved the issue I had with my Python version.
> I can use the NFE toolkit on both sander and pmemd to do steered MD
> simulations, however as I remember, the pmemd could not perform any QMMM
> runs (there is a &qmmm in my mdin file). Is this still the case in
> Amber16?
> Best,
> Sam
>
> On Thu, Apr 13, 2017 at 12:56 PM, Samaneh Ghassabi Kondalaji <
> saghassabikondalaji.mix.wvu.edu> wrote:
>
> > I guess I'll do that! I am already having lots of issues with my current
> > SMD run! Amber14 works but the simulation now is giving me this error:
> > QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
> > QMMM SCC-DFTB: Convergence could not be achieved in this step.
> > QMMM SCC-DFTB: The calculation will continue, but energies and
> > QMMM SCC-DFTB: forces for this step will not be accurate.
> > I think I need to go back and check my QMMM equilibration again before
> > running SMD. Unfortunately the Amber tutorial on SMD (
> > http://ambermd.org/tutorials/advanced/tutorial10/) does not provide much
> > of information regarding the initial distance RST file, I used makeDIST
> to
> > generate distance between N atom on a lysine and O of a water molecule on
> > my weird system! (http://archive.ambermd.org/201704/0114.html) but
> > makeDIST generated a group restraint of 3 H atoms attached to N on Lysine
> > (-NH3+) and the oxygen atom on water.
> > #
> > # 12 LYS NZ 23 WAT O 1.30 3.50
> > &rst
> > ixpk= 0, nxpk= 0, iat= -1, 270, r1= 0.80, r2= 1.30, r3= 4.20, r4=
> 4.70,
> >
> > rk2=20.0, rk3=1000.0, ir6=1, ialtd=0,
> > igr1= 140, 141, 142,
> > /
> > I run two equilibration simulations: one with the RST between O and H
> > atoms as single group (igr1) and the second one between N atom and O. The
> > one from the group atoms seemed OK but the N and O equilibration lead to
> > strange behaviour and as I visualized it, the bond length between N and H
> > was increasing like crazy! So I got my replicates for SMD from the
> > equilibration of O atom and H-group restraints. However the path on SMD
> run
> > monitors the proton transfer from N to O and has nothing to do with my
> atom
> > selection for the equilibration!
> > Will try to solve this problem first and then move to fixing update
> > issues. Thank you so much for all your wonderful help!
> > Best,
> > Sam
> >
> >
> > On Thu, Apr 13, 2017 at 12:35 PM, Hannes Loeffler <
> > Hannes.Loeffler.stfc.ac.uk> wrote:
> >
> >> I am not sure what your problem there is but my suggestions would be to
> >> do a fresh download of the AmberTools and then start the update process
> >> with the Python tool. But since AmberTools17 are soon to be released
> >> you may want to just wait for that.
> >>
> >> Cheers,
> >> Hannes.
> >>
> >>
> >> On Thu, 13 Apr 2017 12:01:35 -0400
> >> Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
> >>
> >> > Thank you for your fast reply. I remember now, this is update.9! I was
> >> > getting an error like this one
> >> > (http://archive.ambermd.org/201610/0212.html) when I was updating
> >> > before installation and couldn't solve it. Reading through update 4
> >> > and 9 description at the time (way before my need for nscu!), I
> >> > decided to continue without. I will use Amber14 for this particular
> >> > run now but I need to fix the problem for future runs, update and
> >> > recompile. I would greatly appreciate if you have any suggestion on
> >> > how to fix this update issue. Sincerely yours,
> >> > Sam
> >> >
> >> > On Thu, Apr 13, 2017 at 11:40 AM, Hannes Loeffler <
> >> > Hannes.Loeffler.stfc.ac.uk> wrote:
> >> >
> >> > > On Thu, 13 Apr 2017 11:29:59 -0400
> >> > > Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
> >> > >
> >> > > > Dear Amber Users and Developers
> >> > > > I am trying to perform a QMMM SMD simulation to monitor a PT
> >> > > > reaction. I equilibrated my system and obtained replicates,
> >> > > > However when I subject the replicates to SMD using the fallowing
> >> > > > parameters and sander.MPI, it seems like sander is not reading
> >> > > > the ncsu section and the variables.
> >> > >
> >> > > I suppose you have applied the recent updates to AmberTools. The
> >> > > code (now called NFE) has been changed to read all inputs through
> >> > > namelists. See nfe.pdf on http://ambermd.org/bugfixesat.html .
> >> > >
> >> > >
> >> > > Cheers,
> >> > > Hannes.
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> >
> >> >
> >> >
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> > *Samaneh ghassabi kondalaji*
> > *PhD student in Chemistry*
> > *555 CRL, Chemistry department*
> > *West Virginia University *
> > *Morgantown, USA*
> >
> > *E-mail: **saghassabikondalaji.mix.wvu.edu*
> > <saghassabikondalaji.mix.wvu.edu>
> >
> >
>
>
>
> --
> *Samaneh ghassabi kondalaji*
> *PhD student in Chemistry*
> *555 CRL, Chemistry department*
> *West Virginia University *
> *Morgantown, USA*
>
> *E-mail: **saghassabikondalaji.mix.wvu.edu*
> <saghassabikondalaji.mix.wvu.edu>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Mon Apr 17 2017 - 10:30:02 PDT
