Hey Thakur,
for the first case you forgot to change ntr variable to 1, therefore
your restraints are ignored. Your &cntrl section should look like
this:
&cntrl
imin=1, maxcyc=10000,
ntc=1, ntf=1, ntb=1, ntpr=5,
ifqnt=1
ntr=1
restraint_wt=100.0,
restraintmask=':2658 & !.H'
/
On the other hand, if you prefer NMR restraints, you must activate
them with nmropt variable in &cntrl section:
nmropt=1
Hope this helps.
Kind regards,
Szymon Żaczek
czw., 30 sie 2018 o 21:06 Thakur, Abhishek <axt651.miami.edu> napisał(a):
>
> Hi everyone,
>
>
> I am doing minimization for Qmmm/MD. But 1 amino acid is moving away. So I want to constrain it. The script that I am using for this is
>
>
> &cntrl
>
> imin=1, maxcyc=10000,
>
> ntc=1, ntf=1, ntb=1, ntpr=5,
>
> ifqnt=1
>
> restraint_wt=100.0,
>
> restraintmask=':2658 & !.H'
>
> /
>
> &qmmm
>
> iqmatoms=8442,8443,8444,8445,8446,8447,8448,8449,8450,8451,8452,8453,8454,8459,8460,8461,8462,8463,8464,8465,8466,8467,8468,8469,8507,8508,8509,8510,8511,8512,8513,8514,8515,8516,8517,8518,8519,9392,9393,9394,9395,9396,9397,9398,9399,9400,9401,9402,11025,11043,11044,11045,11046,11047,11048,11049,11050,11061,11062,11063,11064,
>
> qmcharge=0,
>
> qm_theory='SCC-DFTB',
>
> qmshake=1,
>
> qm_ewald=1, qm_pme=1,
>
> writepdb=1
>
> /
>
> EOF
>
>
>
>
> mpirun -np 16 $AMBERHOME/bin/sander.MPI -O -i mdin -p parm -c restrt -r RP_minAll.rst -o RP_minAll.out -ref restrt
>
>
>
> But while checking the output file I am finding that restrain is not working.
>
> Can anyone suggest me what should I do. I have also tried distance constrain but this also does not work.
>
>
> &rst
>
> iat=5320,5406
>
> r1=0.0, r2=3.9, r3=3.9, r4=99.0,
>
> rk2=400.0, rk3=400.0,
>
>
> As you can see the output file result of minimization below
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 865 -3.0590E+05 2.4259E-01 2.8094E+01 CG 8447
>
>
> BOND = 21840.7418 ANGLE = 1285.9401 DIHED = 8268.1928
>
> VDWAALS = 49919.0852 EEL = -409812.7884 HBOND = 0.0000
>
> 1-4 VDW = 2309.8158 1-4 EEL = 28102.6890 RESTRAINT = 0.0000
>
> DFTBESCF= -7812.0081
>
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Received on Thu Aug 30 2018 - 13:30:02 PDT
