From NWChem
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Just Got Here
Threads 2
Posts 2
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| 6:06:05 AM PST - Fri, Feb 21st 2014 |
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Hello! I try to prepare fragment file for qm/mm calculation with this manual. But when i run prepare, nwchem show me:At line 189 of file pre_pdbseq.F
Fortran runtime error: Bad value during floating point read .
File with prepare:
start qmmm1_prep
prepare
source qmmm1.pdb
new_top new_seq
new_rst
modify segment 1 quantum
update lists
ignore
write qmmm1_ref.pdb
write qmmm1_ref.rst
end
task prepare
qmmm1.pdb:
ATOM 1 C1 NN3 1 3.225 1.586 -2.952 1.00 0.00 C
ATOM 2 C2 NN3 1 4.216 1.195 -2.169 1.00 0.00 C
ATOM 3 C3 NN3 1 1.946 1.212 -2.308 1.00 0.00 C
ATOM 4 C4 NN3 1 3.634 0.549 -0.971 1.00 0.00 C
ATOM 5 N1 NN3 1 2.272 0.596 -1.127 1.00 0.00 N
ATOM 6 H1 NN3 1 3.262 2.089 -3.897 1.00 0.00 H
ATOM 7 H2 NN3 1 5.272 1.294 -2.306 1.00 0.00 H
ATOM 8 H3 NN3 1 1.609 0.228 -0.474 1.00 0.00 H
ATOM 9 N2 NN3 1 0.817 1.456 -2.827 1.00 0.00 N
ATOM 10 C5 NN3 1 3.762 -0.512 1.071 1.00 0.00 C
ATOM 11 C6 NN3 1 3.361 -1.605 3.143 1.00 0.00 C
ATOM 12 N3 NN3 1 2.529 -0.694 1.323 1.00 0.00 N
ATOM 13 N4 NN3 1 2.290 -1.328 2.508 1.00 0.00 N
ATOM 14 S1 NN3 1 4.819 -1.110 2.332 1.00 0.00 S
ATOM 15 N5 NN3 1 4.338 0.075 -0.032 1.00 0.00 N
ATOM 16 N6 NN3 1 3.377 -2.180 4.385 1.00 0.00 N
ATOM 17 H4 NN3 1 2.482 -2.525 4.657 1.00 0.00 H
ATOM 18 H5 NN3 1 4.119 -2.819 4.566 1.00 0.00 H
ATOM 19 C7 NN3 1 -0.355 1.094 -2.204 1.00 0.00 C
ATOM 20 C8 NN3 1 -2.623 0.724 -1.596 1.00 0.00 C
ATOM 21 N7 NN3 1 -0.493 0.487 -1.087 1.00 0.00 N
ATOM 22 N8 NN3 1 -1.789 0.270 -0.742 1.00 0.00 N
ATOM 23 S2 NN3 1 -1.867 1.476 -2.970 1.00 0.00 S
ATOM 24 C9 NN3 1 -4.247 0.033 0.872 1.00 0.00 C
ATOM 25 C10 NN3 1 -5.348 -0.208 1.566 1.00 0.00 C
ATOM 26 C11 NN3 1 -4.643 0.355 -0.526 1.00 0.00 C
ATOM 27 C12 NN3 1 -6.534 -0.063 0.688 1.00 0.00 C
ATOM 28 N9 NN3 1 -6.010 0.285 -0.550 1.00 0.00 N
ATOM 29 H6 NN3 1 -3.229 0.004 1.193 1.00 0.00 H
ATOM 30 H7 NN3 1 -5.438 -0.471 2.600 1.00 0.00 H
ATOM 31 H8 NN3 1 -6.531 0.441 -1.381 1.00 0.00 H
ATOM 32 N10 NN3 1 -3.996 0.661 -1.572 1.00 0.00 N
ATOM 33 N11 NN3 1 -7.721 -0.230 1.045 1.00 0.00 N
ATOM 34 H9 NN3 1 -8.378 -0.082 0.300 1.00 0.00 H
END
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Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 1
Posts 185
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| 7:28:51 PM PDT - Tue, Apr 8th 2014 |
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Hi Ifrit,
Your PDB file is in a wrong format. First of all the data must be in straight columns, hence atoms 25-27 and 32-33 are specified incorrectly. One space in front of NN3 of those atoms should be deleted, simultaneously the column with 1.00 should remain in place. Secondly, the cartesian coordinates of all atoms is one position too far back. The job currently fails on the first atom as it tries to read the coordinates with the format 3f8.3 but the string says " 3.225 1.586 -2.95" which does not match the format string. Hence the error.
Huub
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