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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>
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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*
***********************************************************************
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Received on Fri Oct 19 2018 - 07:30:03 PDT
