Looks like the SCF calculation did not converge. Would you please post the
entire output file to get a proper diagnosis?
Jim Kress
-----Original Message-----
From: Dutta, Ankita via AMBER <amber.ambermd.org>
Sent: Friday, December 6, 2024 10:43 AM
To: amber.ambermd.org
Subject: [AMBER] Convergence failure MCPB.py/GAMESS
Hello all,
I am using the MCPB.py module to optimize the metal site of a CYP450
protein. I am using GAMESS-US to perform geometric optimization. I keep
running into the following error when I perform the initial optimization
using GAMESS . This is specifically for the small model as the MCPB.py
tutorial says to optimize the small model first.
---------------------
ELECTROSTATIC MOMENTS
---------------------
POINT 1 X Y Z (BOHR) CHARGE
24.725363 -4.249575 85.763263 -1.00 (A.U.)
DX DY DZ /D/ (DEBYE)
25.487474 -6.241461 5.729474 26.858780
...... END OF PROPERTY EVALUATION ......
STEP CPU TIME = 4.96 TOTAL CPU TIME = 5420.4 ( 90.3 MIN)
TOTAL WALL CLOCK TIME= 5420.6 SECONDS, CPU UTILIZATION IS 99.99%
***** FAILURE TO LOCATE STATIONARY POINT, SCF HAS NOT CONVERGED
UPDATED HESSIAN, GEOMETRY, AND VECTORS WILL BE PUNCHED FOR RESTART
EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT 01:27:47 06-DEC-2024
9619496 WORDS OF DYNAMIC MEMORY USED
STEP CPU TIME = 0.00 TOTAL CPU TIME = 5420.4 ( 90.3 MIN)
TOTAL WALL CLOCK TIME= 5420.6 SECONDS, CPU UTILIZATION IS 99.99%
DDI Process 0: error code 911
ddikick.x: application process 0 quit unexpectedly.
ddikick.x: Fatal error detected.
The error is most likely to be in the application, so check for input
errors, disk space, memory needs, application bugs, etc.
ddikick.x will now clean up all processes, and exit...
ddikick.x: Sending kill signal to DDI processes.
ddikick.x: Execution terminated due to error(s).
unset echo
----- accounting info -----
Files used on the parent node idsl-gpu were:
-rw-r--r-- 1 ankita ankita 3768 Dec 5 23:57
/home/ankita/gamess/scratch/3ua5_small_opt_tst.F05
-rw-r--r-- 1 ankita ankita 72343920 Dec 6 01:27
/home/ankita/gamess/scratch/3ua5_small_opt_tst.F10
ls: No match.
ls: No match.
ls: No match.
Fri Dec 6 01:27:48 AM UTC 2024
0.114u 0.052s 1:30:21.86 0.0% 0+0k 0+32io 0pf+0w
Input PDB:
ATOM 6644 H1 CYS A 409 10.565 -2.051 48.525 1.00 0.00
ATOM 6645 CH3 CYS A 409 11.027 -2.630 47.725 1.00 0.00
ATOM 6646 H2 CYS A 409 10.504 -3.566 47.530 1.00 0.00
ATOM 6648 CB CYS A 409 12.497 -2.910 48.050 1.00 0.00
ATOM 6649 SG CYS A 409 13.263 -4.175 47.010 1.00 0.00
ATOM 6651 H3 CYS A 409 10.999 -2.034 46.813 1.00 0.00
ATOM 6652 HB2 CYS A 409 13.006 -2.059 47.937 1.00 0.00
ATOM 6653 HB3 CYS A 409 12.551 -3.210 49.001 1.00 0.00
ATOM 6654 HG CYS A 409 13.348 -5.026 47.529 1.00 0.00
HETATM 7537 CHA HEM A 466 11.533 -0.517 45.062 1.00 0.00
HETATM 7538 CHB HEM A 466 15.653 -1.040 47.319 1.00 0.00
HETATM 7539 CHC HEM A 466 16.595 -4.892 44.817 1.00 0.00
HETATM 7540 CHD HEM A 466 12.380 -4.562 42.807 1.00 0.00
HETATM 7541 C1A HEM A 466 12.637 -0.360 45.796 1.00 0.00
HETATM 7542 C2A HEM A 466 12.866 0.840 46.507 1.00 0.00
HETATM 7543 C3A HEM A 466 13.992 0.706 47.135 1.00 0.00
HETATM 7544 C4A HEM A 466 14.495 -0.588 46.842 1.00 0.00
HETATM 7545 CMA HEM A 466 14.642 1.758 48.018 1.00 0.00
HETATM 7546 CAA HEM A 466 11.944 2.055 46.508 1.00 0.00
HETATM 7547 CBA HEM A 466 10.922 1.973 47.614 1.00 0.00
HETATM 7548 CGA HEM A 466 10.509 3.337 47.970 1.00 0.00
HETATM 7549 O1A HEM A 466 9.818 3.912 47.164 1.00 0.00
HETATM 7550 O2A HEM A 466 10.857 3.836 49.039 1.00 0.00
HETATM 7551 C1B HEM A 466 16.220 -2.121 46.765 1.00 0.00
HETATM 7552 C2B HEM A 466 17.520 -2.564 47.102 1.00 0.00
HETATM 7553 C3B HEM A 466 17.767 -3.617 46.405 1.00 0.00
HETATM 7554 C4B HEM A 466 16.633 -3.856 45.629 1.00 0.00
HETATM 7555 CMB HEM A 466 18.458 -1.904 48.096 1.00 0.00
HETATM 7556 CAB HEM A 466 19.018 -4.498 46.352 1.00 0.00
HETATM 7557 CBB HEM A 466 19.907 -4.564 47.333 1.00 0.00
HETATM 7558 C1C HEM A 466 15.497 -5.075 44.112 1.00 0.00
HETATM 7559 C2C HEM A 466 15.355 -6.199 43.268 1.00 0.00
HETATM 7560 C3C HEM A 466 14.205 -6.099 42.730 1.00 0.00
HETATM 7561 C4C HEM A 466 13.601 -4.908 43.218 1.00 0.00
HETATM 7562 CMC HEM A 466 16.344 -7.326 43.007 1.00 0.00
HETATM 7563 CAC HEM A 466 13.632 -7.077 41.712 1.00 0.00
HETATM 7564 CBC HEM A 466 12.577 -7.807 42.006 1.00 0.00
HETATM 7565 C1D HEM A 466 11.810 -3.456 43.243 1.00 0.00
HETATM 7566 C2D HEM A 466 10.527 -3.088 42.832 1.00 0.00
HETATM 7567 C3D HEM A 466 10.236 -1.824 43.546 1.00 0.00
HETATM 7568 C4D HEM A 466 11.398 -1.588 44.293 1.00 0.00
HETATM 7569 CMD HEM A 466 9.617 -3.832 41.862 1.00 0.00
HETATM 7570 CAD HEM A 466 8.975 -0.978 43.445 1.00 0.00
HETATM 7571 CBD HEM A 466 7.813 -1.796 43.930 1.00 0.00
HETATM 7572 CGD HEM A 466 6.868 -0.754 44.329 1.00 0.00
HETATM 7573 O1D HEM A 466 5.765 -1.024 44.748 1.00 0.00
HETATM 7574 O2D HEM A 466 7.252 0.380 44.179 1.00 0.00
HETATM 7575 NA HEM A 466 13.656 -1.276 45.986 1.00 0.00
HETATM 7576 NB HEM A 466 15.644 -2.937 45.819 1.00 0.00
HETATM 7577 NC HEM A 466 14.411 -4.235 44.111 1.00 0.00
HETATM 7578 ND HEM A 466 12.350 -2.567 44.128 1.00 0.00
HETATM 7579 HMA1 HEM A 466 15.164 1.322 48.710 1.00 0.00
HETATM 7580 HMA2 HEM A 466 13.955 2.306 48.429 1.00 0.00
HETATM 7581 HMA3 HEM A 466 15.223 2.319 47.480 1.00 0.00
HETATM 7582 HMB1 HEM A 466 18.288 -0.949 48.116 1.00 0.00
HETATM 7583 HMB2 HEM A 466 19.377 -2.063 47.829 1.00 0.00
HETATM 7584 HMB3 HEM A 466 18.309 -2.277 48.979 1.00 0.00
HETATM 7585 HMC1 HEM A 466 15.860 -8.141 42.801 1.00 0.00
HETATM 7586 HMC2 HEM A 466 16.890 -7.466 43.796 1.00 0.00
HETATM 7587 HMC3 HEM A 466 16.913 -7.090 42.258 1.00 0.00
HETATM 7588 HMD1 HEM A 466 10.157 -4.313 41.215 1.00 0.00
HETATM 7589 HMD2 HEM A 466 9.049 -3.197 41.399 1.00 0.00
HETATM 7590 HMD3 HEM A 466 9.065 -4.461 42.353 1.00 0.00
HETATM 7591 HBB1 HEM A 466 20.683 -5.140 47.247 1.00 0.00
HETATM 7592 HBB2 HEM A 466 19.782 -4.037 48.137 1.00 0.00
HETATM 7593 HBC1 HEM A 466 12.219 -8.427 41.352 1.00 0.00
HETATM 7594 HBC2 HEM A 466 12.158 -7.725 42.877 1.00 0.00
HETATM 7595 HBA1 HEM A 466 11.297 1.522 48.387 1.00 0.00
HETATM 7596 HBA2 HEM A 466 10.155 1.453 47.326 1.00 0.00
HETATM 7597 HAA1 HEM A 466 11.492 2.120 45.652 1.00 0.00
HETATM 7598 HAA2 HEM A 466 12.471 2.862 46.612 1.00 0.00
HETATM 7599 HBD1 HEM A 466 8.056 -2.371 44.672 1.00 0.00
HETATM 7600 HBD2 HEM A 466 7.453 -2.368 43.234 1.00 0.00
HETATM 7601 HAD1 HEM A 466 8.830 -0.697 42.528 1.00 0.00
HETATM 7602 HAD2 HEM A 466 9.066 -0.172 43.978 1.00 0.00
HETATM 7603 HHA HEM A 466 10.860 0.124 45.090 1.00 0.00
HETATM 7604 HHB HEM A 466 16.066 -0.609 48.032 1.00 0.00
HETATM 7605 HHC HEM A 466 17.317 -5.473 44.744 1.00 0.00
HETATM 7606 HHD HEM A 466 11.926 -5.107 42.206 1.00 0.00
HETATM 7607 HAB HEM A 466 19.168 -5.036 45.559 1.00 0.00
HETATM 7608 HAC HEM A 466 14.048 -7.162 40.840 1.00 0.00
HETATM 7609 FE FE A 467 14.037 -2.617 45.085 1.00 0.00
Gamess input file produced by mcpb.py module
$SYSTEM MEMDDI=400 MWORDS=200 $END
$CONTRL DFTTYP=B3LYP SCFTYP=UHF RUNTYP=OPTIMIZE ICHARG=-1 MULT=2 $END
$STATPT NSTEP=1000 OPTTOL=0.0005 $END $trans dirtrf=.t. $END $BASIS
GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $DATA Cluster/6-31G
C1
H 1.0 10.565 -2.051 48.525
C 6.0 11.027 -2.630 47.725
H 1.0 10.504 -3.566 47.530
C 6.0 12.497 -2.910 48.050
S 16.0 13.263 -4.175 47.010
H 1.0 10.999 -2.034 46.813
H 1.0 13.006 -2.059 47.937
H 1.0 12.551 -3.210 49.001
H 1.0 13.348 -5.026 47.529
C 6.0 11.533 -0.517 45.062
C 6.0 15.653 -1.040 47.319
C 6.0 16.595 -4.892 44.817
C 6.0 12.380 -4.562 42.807
C 6.0 12.637 -0.360 45.796
C 6.0 12.866 0.840 46.507
C 6.0 13.992 0.706 47.135
C 6.0 14.495 -0.588 46.842
C 6.0 14.642 1.758 48.018
C 6.0 11.944 2.055 46.508
C 6.0 10.922 1.973 47.614
C 6.0 10.509 3.337 47.970
O 8.0 9.818 3.912 47.164
O 8.0 10.857 3.836 49.039
C 6.0 16.220 -2.121 46.765
C 6.0 17.520 -2.564 47.102
C 6.0 17.767 -3.617 46.405
C 6.0 16.633 -3.856 45.629
C 6.0 18.458 -1.904 48.096
C 6.0 19.018 -4.498 46.352
C 6.0 19.907 -4.564 47.333
C 6.0 15.497 -5.075 44.112
C 6.0 15.355 -6.199 43.268
C 6.0 14.205 -6.099 42.730
C 6.0 13.601 -4.908 43.218
C 6.0 16.344 -7.326 43.007
C 6.0 13.632 -7.077 41.712
C 6.0 12.577 -7.807 42.006
C 6.0 11.810 -3.456 43.243
C 6.0 10.527 -3.088 42.832
C 6.0 10.236 -1.824 43.546
C 6.0 11.398 -1.588 44.293
C 6.0 9.617 -3.832 41.862
C 6.0 8.975 -0.978 43.445
C 6.0 7.813 -1.796 43.930
C 6.0 6.868 -0.754 44.329
O 8.0 5.765 -1.024 44.748
O 8.0 7.252 0.380 44.179
N 7.0 13.656 -1.276 45.986
N 7.0 15.644 -2.937 45.819
N 7.0 14.411 -4.235 44.111
N 7.0 12.350 -2.567 44.128
H 1.0 15.164 1.322 48.710
H 1.0 13.955 2.306 48.429
H 1.0 15.223 2.319 47.480
H 1.0 18.288 -0.949 48.116
H 1.0 19.377 -2.063 47.829
H 1.0 18.309 -2.277 48.979
H 1.0 15.860 -8.141 42.801
H 1.0 16.890 -7.466 43.796
H 1.0 16.913 -7.090 42.258
H 1.0 10.157 -4.313 41.215
H 1.0 9.049 -3.197 41.399
H 1.0 9.065 -4.461 42.353
H 1.0 20.683 -5.140 47.247
H 1.0 19.782 -4.037 48.137
H 1.0 12.219 -8.427 41.352
H 1.0 12.158 -7.725 42.877
H 1.0 11.297 1.522 48.387
H 1.0 10.155 1.453 47.326
H 1.0 11.492 2.120 45.652
H 1.0 12.471 2.862 46.612
H 1.0 8.056 -2.371 44.672
H 1.0 7.453 -2.368 43.234
H 1.0 8.830 -0.697 42.528
H 1.0 9.066 -0.172 43.978
H 1.0 10.860 0.124 45.090
H 1.0 16.066 -0.609 48.032
H 1.0 17.317 -5.473 44.744
H 1.0 11.926 -5.107 42.206
H 1.0 19.168 -5.036 45.559
H 1.0 14.048 -7.162 40.840
Fe 26.0 14.037 -2.617 45.085
$END
I have made some small adjustments to the input file as you can see, in that
I have increased the default OPTTOL variable from 0.0002 to 0.0005.
I am not sure what else I can try. Any help with this will be appreciated!
Also happy to provide more information!
Best,
Ankita
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Received on Fri Dec 06 2024 - 10:00:02 PST
