On Fri, Oct 19, 2018 at 9:28 AM Vito GENNA <vito.genna.irbbarcelona.org>
wrote:
> Hi Zuo,
>
> You are right, there are 4 atoms but there is also the *rstwt* keywords to
> define a function of multiple distance restraints, called a "generalized
> distance coordinate" restraint.
> This is the formalism to define the asymmetrical mono-dimensional reaction
> coordinate.
>
> V
>
> On Fri, Oct 19, 2018 at 4:23 PM Zuo, Zhicheng <Zhicheng.Zuo.unthsc.edu>
> wrote:
>
> > Hi, I not not familiar with QM/MM simulation. In your MD.IN file, yet,
> >
> > I noticed that "iat=487,31,31,40" actually corresponds to four atoms.
> >
> > I think you should specify two atoms for distance restraint.
> >
> > Hope it works for you. Good luck!
> >
> >
> > Best
> >
> > Zhicheng Zuo
> >
> > ________________________________
> > From: Vito GENNA <vito.genna.irbbarcelona.org>
> > Sent: Friday, October 19, 2018 6:29:12 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] Constrained QM.MM minimization
> >
> > Dear AMBERusers,
> >
> > I am writing you because I am experiencing a weird behave in my
> > calculations.
> > My goal is to generates the seeds for a subsequent umbrella sampling
> > calculation and to do so, I gonna first reconstruct the potential energy
> > surface with a series of minimized structures.
> >
> > I am using a mono-dimensional and asymmetric reaction coordinate (RC)
> > (widely used for this kind of SN2-type reactions).
> >
> > *Here the input file:*
> > *-----------------------------------------------*
> > PES
> > &cntrl
> > imin=1, maxcyc=500, ntmin=3,
> > ntpr=2, ntb=0, cut=10,
> > ifqnt=1, drms=1E-02,
> > nmropt = 1,
> > &end
> > &qmmm
> > qmmask='.1-50, 468-500, 7643-7648, 9907-9912, 7653-7654, 7669-7670,
> > 8598-8607, 8519-8530, 7681-7692, 76568-76570, 83522-83524',
> > qmcharge=+1,
> > spin=1,
> > qm_theory='EXTERN'
> > qmshake=0,
> > qm_ewald=0,
> > writepdb=1,
> > &end
> > &tc
> > method = 'BLYP',
> > basis = '6-31g*',
> > maxit = 2000,
> > /
> > &wt
> > type='DUMPFREQ', istep1=1,
> > &end
> > &wt
> > type='END',
> > &end
> > DISANG=rst_-1.7
> > DUMPAVE=rst_-1.7.dat
> > LISTIN=POUT
> > LISTOUT=POUT
> > *-----------------------------------------------*
> >
> > here the* rst_-1.7 *file:
> > *-----------------------------------------------*
> > &rst iat=487,31,31,40, r1=-2.2, r2=-1.7, r3=-1.7, r4=-1.2,
> rstwt=-1.0,1.0,
> > rk2=300.0, rk3=300.0, /
> > *-----------------------------------------------*
> > in order to apply an harmonic potential with a well centered on -1.7 (the
> > RC)
> >
> > But, for some mysterious (at least to me) reaons, I got the following RC1
> > values along the calculations:
> >
> > here the* rst_-1.7.dat *file:
> > *-----------------------------------------------*
> > 0 -1.888
> > 1 -1.190
> > 2 -1.802
> > 3 -1.887
> > 4 -1.888
> > 5 -1.888
> > 6 -1.888
> > 7 -1.193
> > *-----------------------------------------------*
> > Of course, fluctuations are expected and wanter in order to reconstruct
> the
> > PMF but I never get a structure in which the RC value is ~-1.7.
> Similarly,
> > for subsequent windows, -1.5, -1.3 and so on...
> >
> > This is the command I run:
> >
> > *sander -O -i min_-1.7.in <http://min_-1.7.in> -o min_-1.7.out -p
> > sys.prmtop -c fixed_-1.9.rst7 -r out_-1.7.rst7*
> >
> > Note that *fixed_-1.9.rst7 *comes from a previous calculations in which
> > -1.9 was the RC1 desired value and that was finely obtained.
> > I am thinking perhaps something is getting wrong with the input file
> > format....possible?
> >
> > Have you got any idea?
> >
> > Thanks in advance
> >
> > Vito
> >
> > PS: terachem1.94, amber14
> >
> > --
> >
> > ***********************************************************************
> > *Vito Genna, Ph.D*
> > *EMBO Fellow*
> >
> > *Postoctoral Researcher*
> >
> > *Molecular Modeling and Bioinformatics*
> > *Orozco Lab*
> >
> > *Institute for Research in Biomedicine (IRB Barcelona)*
> >
> > *Parc Centific de Barcelona*
> >
> > *C/ Baldiri Reixac 10-12*
> > *08028 Barcelona*
> >
> > ***********************************************************************
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> > AMBER.ambermd.org
> >
> >
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> >
>
>
> --
>
> ***********************************************************************
> *Vito Genna, Ph.D*
> *EMBO Fellow*
>
> *Postoctoral Researcher*
>
> *Molecular Modeling and Bioinformatics*
> *Orozco Lab*
>
> *Institute for Research in Biomedicine (IRB Barcelona)*
>
> *Parc Centific de Barcelona*
>
> *C/ Baldiri Reixac 10-12*
> *08028 Barcelona*
>
> ***********************************************************************
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 19 2018 - 08:00:02 PDT
