I am trying to run antechamber on NADH (see below for the file).
I prepared the pdb file with pdb4amber and also ran acdoctor without any
problems.
Nevertheless I get an error when using -c bcc:
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1920E+07 DeltaE = 0.8865E+01 DeltaP = 0.7404E+00
QMMM: Smallest DeltaE = 0.7915E-01 DeltaP = 0.3263E+00 Step = 177
I tried changing sqm.in grms_tol=0.0005, scfconv=1.d-10, as described in
the manual.
Running antechamber without any -c flag gives me no errors.
Why is -c bcc not working?
What happens if I do not use any -c flag?
Additional question:
How is gaff2 better than gaff? Should I use gaff2 by default? Is there
any literature on that?
PDB FILE:
HETATM 5420 P1 L01 900 7.880 48.872 17.769 1.00
0.00 P
HETATM 5421 P2 L01 900 6.020 47.922 15.340 1.00
0.00 P
HETATM 5422 O1 L01 900 11.942 47.657 18.909 1.00
0.00 O
HETATM 5423 O2 L01 900 2.913 50.735 16.710 1.00
0.00 O
HETATM 5424 O3 L01 900 9.495 48.339 17.472 1.00
0.00 O
HETATM 5425 O4 L01 900 11.861 46.521 21.949 1.00
0.00 O
HETATM 5426 O5 L01 900 7.043 47.867 16.691 1.00
0.00 O
HETATM 5427 O6 L01 900 9.125 46.772 20.968 1.00
0.00 O
HETATM 5428 O7 L01 900 4.883 49.055 15.935 1.00
0.00 O
HETATM 5429 O8 L01 900 1.317 51.905 19.631 1.00
0.00 O
HETATM 5430 O9 L01 900 2.814 49.522 20.010 1.00
0.00 O
HETATM 5431 O10 L01 900 7.478 48.451 19.166 1.00
0.00 O
HETATM 5432 O11 L01 900 7.774 50.294 17.276 1.00
0.00 O1-
HETATM 5433 O12 L01 900 6.728 48.593 14.189 1.00
0.00 O
HETATM 5434 O13 L01 900 5.335 46.580 15.212 1.00
0.00 O1-
HETATM 5435 O14 L01 900 1.086 51.183 12.537 1.00
0.00 O
HETATM 5436 N1 L01 900 12.925 49.486 20.136 1.00
0.00 N
HETATM 5437 N2 L01 900 14.267 51.255 20.320 1.00
0.00 N
HETATM 5438 N3 L01 900 10.876 50.657 19.436 1.00
0.00 N
HETATM 5439 N4 L01 900 1.333 52.492 16.497 1.00
0.00 N
HETATM 5440 N5 L01 900 11.166 53.056 19.426 1.00
0.00 N
HETATM 5441 N6 L01 900 13.164 54.125 19.910 1.00
0.00 N
HETATM 5442 N7 L01 900 0.252 53.097 11.878 1.00
0.00 N
HETATM 5443 C1 L01 900 12.472 48.038 20.150 1.00
0.00 C
HETATM 5444 C2 L01 900 12.171 50.586 19.821 1.00
0.00 C
HETATM 5445 C3 L01 900 11.441 47.684 21.235 1.00
0.00 C
HETATM 5446 C4 L01 900 13.022 51.660 19.990 1.00
0.00 C
HETATM 5447 C5 L01 900 10.735 46.923 19.088 1.00
0.00 C
HETATM 5448 C6 L01 900 10.181 47.525 20.377 1.00
0.00 C
HETATM 5449 C7 L01 900 14.159 49.952 20.415 1.00
0.00 C
HETATM 5450 C8 L01 900 2.237 51.767 17.359 1.00
0.00 C
HETATM 5451 C9 L01 900 12.462 52.944 19.776 1.00
0.00 C
HETATM 5452 C10 L01 900 1.494 51.047 18.501 1.00
0.00 C
HETATM 5453 C11 L01 900 3.541 49.939 17.693 1.00
0.00 C
HETATM 5454 C12 L01 900 2.374 49.778 18.683 1.00
0.00 C
HETATM 5455 C13 L01 900 9.851 47.010 17.824 1.00
0.00 C
HETATM 5456 C14 L01 900 10.478 51.924 19.250 1.00
0.00 C
HETATM 5457 C15 L01 900 4.055 48.661 17.018 1.00
0.00 C
HETATM 5458 C16 L01 900 1.150 52.063 15.190 1.00
0.00 C
HETATM 5459 C17 L01 900 1.017 53.797 16.825 1.00
0.00 C
HETATM 5460 C18 L01 900 0.831 52.883 14.160 1.00
0.00 C
HETATM 5461 C19 L01 900 0.685 54.719 15.896 1.00
0.00 C
HETATM 5462 C20 L01 900 0.593 54.396 14.396 1.00
0.00 C
HETATM 5463 C21 L01 900 0.744 52.325 12.824 1.00
0.00 C
HETATM 5464 H1 L01 900 12.587 46.739 22.541 1.00
0.00 H
HETATM 5465 H2 L01 900 8.297 47.017 20.538 1.00
0.00 H
HETATM 5466 H3 L01 900 0.758 51.440 20.269 1.00
0.00 H
HETATM 5467 H4 L01 900 2.054 49.627 20.607 1.00
0.00 H
HETATM 5468 H5 L01 900 13.931 54.093 20.560 1.00
0.00 H
HETATM 5469 H6 L01 900 12.551 54.929 19.945 1.00
0.00 H
HETATM 5470 H7 L01 900 0.194 52.717 10.950 1.00
0.00 H
HETATM 5471 H8 L01 900 -0.035 54.046 12.070 1.00
0.00 H
HETATM 5472 H9 L01 900 13.380 47.450 20.302 1.00
0.00 H
HETATM 5473 H10 L01 900 11.314 48.527 21.907 1.00
0.00 H
HETATM 5474 H11 L01 900 10.993 45.876 19.269 1.00
0.00 H
HETATM 5475 H12 L01 900 9.814 48.528 20.167 1.00
0.00 H
HETATM 5476 H13 L01 900 14.948 49.274 20.710 1.00
0.00 H
HETATM 5477 H14 L01 900 3.023 52.408 17.765 1.00
0.00 H
HETATM 5478 H15 L01 900 0.515 50.732 18.130 1.00
0.00 H
HETATM 5479 H16 L01 900 4.381 50.487 18.119 1.00
0.00 H
HETATM 5480 H17 L01 900 1.769 48.928 18.360 1.00
0.00 H
HETATM 5481 H18 L01 900 8.973 46.370 17.927 1.00
0.00 H
HETATM 5482 H19 L01 900 10.416 46.601 16.986 1.00
0.00 H
HETATM 5483 H20 L01 900 9.461 52.046 18.907 1.00
0.00 H
HETATM 5484 H21 L01 900 4.615 48.071 17.745 1.00
0.00 H
HETATM 5485 H22 L01 900 3.235 48.047 16.644 1.00
0.00 H
HETATM 5486 H23 L01 900 1.306 51.002 15.040 1.00
0.00 H
HETATM 5487 H24 L01 900 1.053 54.033 17.882 1.00
0.00 H
HETATM 5488 H25 L01 900 0.460 55.722 16.231 1.00
0.00 H
HETATM 5489 H26 L01 900 1.323 54.990 13.842 1.00
0.00 H
HETATM 5490 H27 L01 900 -0.398 54.683 14.041 1.00
0.00 H
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
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Received on Thu Dec 08 2016 - 08:00:02 PST
