Dear Amber users
I am trying to minimize protein in different minimization steps by keeping
restraint weight on heavy atoms. The input file is as below mentioned:-
Minimization with Cartesian restraints for the solute
&cntrl
imin=1, maxcyc=50000,
ntmin=1, ncyc= 10000,
ntpr=5,
ntr=1,
&end
Group input for restrained atoms
restraint_wt=25, // Cartesian restraint
restraintmask=':1-492',
&end
END
END
but in output, the restraints are not being picked up.
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8216E+05 1.6069E+02 4.3837E+04 HE1 7053
BOND = 378.4475 ANGLE = 1257.5102 DIHED =
6263.3382
VDWAALS = 27835.5289 EEL = -238497.5576 HBOND =
0.0000
1-4 VDW = 2639.8382 1-4 EEL = 17966.0709 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 -1.8504E+05 5.8051E+01 1.4620E+04 HE1 7053
BOND = 378.2588 ANGLE = 1256.8232 DIHED =
6263.2473
VDWAALS = 24988.7515 EEL = -238536.0582 HBOND =
0.0000
1-4 VDW = 2639.5797 1-4 EEL = 17965.8675 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
10 -1.8746E+05 1.7765E+01 1.9485E+03 HE1 7053
BOND = 384.2512 ANGLE = 1250.0565 DIHED =
6262.3632
VDWAALS = 22974.9572 EEL = -238930.2273 HBOND =
0.0000
1-4 VDW = 2636.7705 1-4 EEL = 17963.7135 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
15 -1.9034E+05 1.1909E+01 4.4730E+02 HD23 3880
BOND = 534.0545 ANGLE = 1220.1833 DIHED =
6257.8817
VDWAALS = 21867.6042 EEL = -240800.5609 HBOND =
0.0000
1-4 VDW = 2622.8725 1-4 EEL = 17953.5035 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
20 -1.9551E+05 8.3383E+00 1.3675E+02 OD1 1557
BOND = 1873.9806 ANGLE = 1153.4849 DIHED =
6245.9053
VDWAALS = 20698.3690 EEL = -245985.4040 HBOND =
0.0000
1-4 VDW = 2583.3788 1-4 EEL = 17923.6629 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
25 -2.0338E+05 4.4180E+00 5.2188E+01 OD1 1557
BOND = 6900.1912 ANGLE = 1085.4016 DIHED =
6229.3123
VDWAALS = 18981.2595 EEL = -256911.7772 HBOND =
0.0000
1-4 VDW = 2492.5840 1-4 EEL = 17844.2183 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
30 -2.1353E+05 2.5465E+00 2.0357E+01 HE2 3793
BOND = 11222.4078 ANGLE = 1098.0334 DIHED =
6243.1241
VDWAALS = 17370.6863 EEL = -269419.7905 HBOND =
0.0000
1-4 VDW = 2299.7255 1-4 EEL = 17651.8788 RESTRAINT =
0.0000
Could you please guide 1what is missing in the input syntax due to which I
am not getting restraint force?
Regards
Sadaf
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Received on Thu Aug 12 2021 - 17:30:02 PDT
