| 4:44:16 AM PDT - Tue, Oct 20th 2015 |
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Dear all,
My qmmm system has two groups inside a protein defined as quantum, a CO3 ion and a FE ion.
During the prepare job, the FE atom always moves away to weird coordinates, far away from the starting place, but the CO3 stays in place. Needless to say, in reality they stick together inside the protein.
Any ideas why this happens?
If I run a qmmm dft optimization on this crazy system, it converges ok, and the FE ion remains in the weird coordinantes.
I'm enclosing links to the script and source files, coulnd't figure out how to upload them here.
source_pdb
script_file
Thanks for the attention,
Pd
PS - I checked the pdb file format. it looks ok, even when I compare it with the N3o3.pdb file on nwchem documentation:
N3o3.pdb
ATOM 1 O1 NN3 1 1.562 0.180 -1.368
ATOM 2 N1 NN3 1 1.316 0.936 -0.424
ATOM 3 N2 NN3 1 2.364 1.026 0.488
ATOM 4 O2 NN3 1 3.472 0.429 0.421
ATOM 5 N3 NN3 1 1.958 1.906 1.488
ATOM 6 O3 NN3 1 2.814 2.068 2.361
source pdb file
ATOM 1 N ASP A 3 33.430 27.007 61.687 0.0782 1.8240
ATOM 2 CA ASP A 3 32.228 27.083 60.871 0.0292 1.9080
ATOM 3 C ASP A 3 31.484 28.448 61.015 0.5621 1.9080
[...]
ATOM 5021 HA CYS A 331 55.791 72.564 61.090 0.0938 1.3870
ATOM 5022 HB2 CYS A 331 55.200 75.268 60.409 0.1228 1.3870
ATOM 5023 FE FE A 400 49.913 50.743 51.393 1.0000 0.0000
ATOM 5024 C CO3 A 500 49.752 52.852 50.082 1.0000 1.0000
ATOM 5025 O1 CO3 A 500 50.624 52.623 50.963 1.0000 1.0000
ATOM 5026 O2 CO3 A 500 48.843 51.940 49.831 1.0000 1.0000
ATOM 5027 O3 CO3 A 500 49.755 54.000 49.449 1.0000 1.0000
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