[AMBER] Constrained QM.MM minimization

From: Vito GENNA <vito.genna.irbbarcelona.org>
Date: Fri, 19 Oct 2018 15:29:12 +0200

Dear AMBERusers,

I am writing you because I am experiencing a weird behave in my
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:*
  imin=1, maxcyc=500, ntmin=3,
  ntpr=2, ntb=0, cut=10,
  ifqnt=1, drms=1E-02,
  nmropt = 1,
  qmmask='.1-50, 468-500, 7643-7648, 9907-9912, 7653-7654, 7669-7670,
8598-8607, 8519-8530, 7681-7692, 76568-76570, 83522-83524',
  method = 'BLYP',
  basis = '6-31g*',
  maxit = 2000,
  type='DUMPFREQ', istep1=1,

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

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

Have you got any idea?

Thanks in advance


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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Received on Fri Oct 19 2018 - 06:30:02 PDT
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