randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2031 11 1 4.0000
randomi_496_> Amplitude is > 0; randomization is done.
check_inf__E> Atom 206 has out-of-range coordinates (usually infinity).
The objective function can thus not be calculated.
Traceback (most recent call last):
File "/Users/arjun/script/mutate_model.py", line 157, in <module>
optimize(s, sched)
File "/Users/arjun/script/mutate_model.py", line 28, in optimize
step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)
File "/Library/modeller-9.11/modlib/modeller/schedule.py", line 71, in optimize
return o.optimize(atmsel, schedule_scale=self.scale, **vars)
File "/Library/modeller-9.11/modlib/modeller/optimizers/conjugate_gradients.py", line 38, in optimize
ret = func(self._modpt, mdl.modpt, edat.modpt, libs.modpt, inds, **vars)
OverflowError: check_inf__E> Atom 206 has out-of-range coordinates (usually infinity).
The objective function can thus not be calculated.
It generates the following 2a01.pdbARG26.tmp file. I notice 7 atoms of the ARG have"0" value on the last column. What does that mean?
ORIGINAL PDB:
ATOM 203 N GLY A 26 84.766 -21.780 101.354 1.00 23.56 N
ATOM 204 CA GLY A 26 85.026 -21.762 99.961 1.00 25.16 C
ATOM 205 C GLY A 26 86.327 -21.144 99.510 1.00 25.70 C
ATOM 206 O GLY A 26 86.994 -21.670 98.600 1.00 26.35 O
MUTATED MODEL:
ATOM 203 N ARG A 26 84.766 -21.780 101.354 1.00 23.56 N
ATOM 204 CA ARG A 26 85.026 -21.762 99.961 1.00 25.16 C
ATOM 205 CB ARG A 26 83.792 -21.092 99.292 1.00 0.00 C
ATOM 206 CG ARG A 26 83.847 -20.959 97.751 1.00 0.00 C
ATOM 207 CD ARG A 26 82.605 -20.290 97.136 1.00 0.00 C
ATOM 208 NE ARG A 26 82.821 -20.241 95.649 1.00 0.00 N
ATOM 209 CZ ARG A 26 81.927 -19.718 94.798 1.00 0.00 C
ATOM 210 NH1 ARG A 26 82.220 -19.725 93.500 1.00 0.00 N
ATOM 211 NH2 ARG A 26 80.764 -19.224 95.210 1.00 0.00 N
ATOM 212 C ARG A 26 86.327 -21.144 99.510 1.00 25.70 C
ATOM 213 O ARG A 26 86.994 -21.670 98.600 1.00 26.35 O
The script also gave this error when I am trying to mutate to ARG60. Rest of the ARG and other mutations worked on the model.
Would be helpful if someone could explain the error and how may I fix it.
Regards
Arjun
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The dream is not that you see in sleep , dream is which does not let you sleep. ~
Dr. Abdul Kalam (Former President of Republic of India)
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