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 - 12:30:02 PDT
