# Re: [AMBER] Constrained QM.MM minimization

From: Zuo, Zhicheng <Zhicheng.Zuo.unthsc.edu>
Date: Fri, 19 Oct 2018 14:23:00 +0000

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?

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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Received on Fri Oct 19 2018 - 07:30:02 PDT
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