[phenixbb] phenix.elbow with GAMESS
Nigel Moriarty
nwmoriarty at lbl.gov
Tue Mar 1 15:50:19 PST 2016
Fred
The GAMESS run has failed. It should have something like
***** EQUILIBRIUM GEOMETRY LOCATED *****
COORDINATES OF ALL ATOMS ARE (ANGS)
ATOM CHARGE X Y Z
------------------------------------------------------------
CR 24.0 -1.4046704720 -0.0044107654 -0.4346577152
O 8.0 0.3767999588 -0.0356515989 -0.1243040639
H 1.0 1.1070887248 -0.0807544290 0.4885987331
and end with
......END OF GEOMETRY SEARCH......
STEP CPU TIME = 0.00 TOTAL CPU TIME = 13.0 ( 0.2 MIN)
TOTAL WALL CLOCK TIME= 16.0 SECONDS, CPU UTILIZATION IS 81.31%
1046951 WORDS OF DYNAMIC MEMORY USED
EXECUTION OF GAMESS TERMINATED NORMALLY Tue Mar 1 11:03:46 2016
DDI: 262808 bytes (0.3 MB / 0 MWords) used by master data server.
----------------------------------------
CPU timing information for all processes
========================================
0: 12.777090 + 0.248382 = 13.025472
1: 0.001435 + 0.002468 = 0.003903
----------------------------------------
ddikick.x: exited gracefully.
Clearly, I need to have eLBOW point out that the GAMESS job did not finish
gracefully. You can try to add --initial-geometry=ligand.pdb to give GAMESS
a different starting geometry to see if it progresses further.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Tue, Mar 1, 2016 at 2:54 PM, Dyda <dyda at ulti.niddk.nih.gov> wrote:
> Dear Nigel,
>
> I agree, but pdb is what I have. I should think that the quality of the
> input should not
> impact whether .cif is output or not.
>
> The end of .gam:
>
> COORDINATES OF ALL ATOMS ARE (ANGS)
> ATOM CHARGE X Y Z
> ------------------------------------------------------------
> CR 24.0 0.1912339815 -0.0759848760 -0.0714344444
> O 8.0 2.3234578345 -0.2357845497 -0.1508067587
> O 8.0 -0.7105232282 0.0098034893 1.8036685126
> O 8.0 1.2076867850 -0.3346443692 -1.7335283981
> O 8.0 -0.5260639033 1.7906968578 0.3539796904
> O 8.0 0.9068338690 -1.9599479901 -0.6296444533
> O 8.0 -1.9397708185 -0.1141525894 0.1891144601
> C 6.0 2.8515146213 -0.0055174102 1.1989521238
> C 6.0 1.9707450903 -0.6979131843 2.5449414024
> C 6.0 0.4359449408 -0.0451724719 2.8465226464
> C 6.0 3.0118766316 1.4363395032 1.6481146467
> C 6.0 -0.0653144611 0.1564048347 4.4949200023
> C 6.0 0.6249516515 0.4233319450 -2.8992641137
> C 6.0 0.1643384668 2.4470081023 -2.2535061934
> C 6.0 -0.9128640701 2.5088690737 -0.8469830060
> C 6.0 1.5743374229 0.5462852223 -3.8500329514
> C 6.0 -1.2118325877 3.9283584299 -0.4940679455
> C 6.0 -0.1968029455 -3.0386081819 -0.8007813286
> C 6.0 -1.6882650231 -2.4665688184 -1.2935287464
> C 6.0 -2.6276161825 -1.2806785380 -0.2996777905
> C 6.0 -0.3391479898 -3.6453123923 0.6022767778
> C 6.0 -4.1453203443 -1.5862494692 0.1854244826
> H 1.0 3.8553615186 -0.4420315035 1.2332199192
> H 1.0 2.2818981212 -1.6647647766 3.1911897462
> H 1.0 1.9667722755 1.9810594320 1.6970399031
> H 1.0 3.6823942975 1.6618943249 2.5365171626
> H 1.0 3.6238703905 1.9113333115 0.7438740891
> H 1.0 0.8971167594 0.4695270592 5.1329947121
> H 1.0 -0.6645891831 1.2206664940 4.5846682936
> H 1.0 -0.6246971002 -0.6219821332 4.8583146656
> H 1.0 -0.2487681929 -0.1134304045 -3.2439960069
> H 1.0 1.1860397915 3.0186834522 -2.1641816248
> H 1.0 -0.3750591440 2.8925729326 -3.2804399647
> H 1.0 -1.9371292026 2.0739333624 -1.0806155814
> H 1.0 1.9496290579 -0.6216286700 -4.2730835081
> H 1.0 2.4497745286 1.0199721671 -3.6228827183
> H 1.0 1.0277269687 0.9853088788 -4.8324755816
> H 1.0 -1.6488875565 4.5338413808 -1.4704889855
> H 1.0 -1.7951603842 3.9656768136 0.3514485986
> H 1.0 -0.2983062508 4.5239905524 -0.4318350930
> H 1.0 0.1219656972 -3.8775516930 -1.5693737575
> H 1.0 -2.2141859609 -2.6816187114 -2.2405875656
> H 1.0 0.7133579392 -3.9124935444 1.0380228614
> H 1.0 -0.7783653014 -2.9666445248 1.3120392457
> H 1.0 -0.9150821609 -4.6238970562 0.5814496583
> H 1.0 -4.2320258907 -2.8021018481 0.2370382406
> H 1.0 -4.7833967302 -1.1881592471 -0.7055025179
> H 1.0 -4.4126745266 -1.1246420328 1.0220077683
>
> ********************
> 1 ELECTRON INTEGRALS
> ********************
> ...... END OF ONE-ELECTRON INTEGRALS ......
> CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0
> MIN)
> TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 100.00%
>
> -------------
> GUESS OPTIONS
> -------------
> GUESS =HUCKEL NORB = 0 NORDER= 0
> MIX = F PRTMO = F PUNMO = F
> TOLZ = 1.0E-08 TOLE = 1.0E-05
> SYMDEN= F PURIFY= F
>
> INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.
> HUCKEL GUESS REQUIRES 649929 WORDS.
>
> SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S).
> 94 ORBITALS ARE OCCUPIED ( 30 CORE ORBITALS).
> 31=A 32=A 33=A 34=A 35=A 36=A 37=A
> 38=A 39=A 40=A 41=A 42=A 43=A 44=A
> 45=A 46=A 47=A 48=A 49=A 50=A 51=A
> 52=A 53=A 54=A 55=A 56=A 57=A 58=A
> 59=A 60=A 61=A 62=A 63=A 64=A 65=A
> 66=A 67=A 68=A 69=A 70=A 71=A 72=A
> 73=A 74=A 75=A 76=A 77=A 78=A 79=A
> 80=A 81=A 82=A 83=A 84=A 85=A 86=A
> 87=A 88=A 89=A 90=A 91=A 92=A 93=A
> 94=A 95=A 96=A 97=A 98=A 99=A 100=A
> 101=A 102=A 103=A 104=A
> ...... END OF INITIAL ORBITAL SELECTION ......
> CPU 0: STEP CPU TIME= 0.24 TOTAL CPU TIME= 0.3 ( 0.0
> MIN)
> TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.49%
>
> ----------------------
> AO INTEGRAL TECHNOLOGY
> ----------------------
> S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY
> KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR).
> S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY
> KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE).
> S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5,
> ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED
> SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER).
> S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY
> MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY).
>
> --------------------
> 2 ELECTRON INTEGRALS
> --------------------
>
> DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK.
> DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK.
> ...... END OF TWO-ELECTRON INTEGRALS .....
> CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 0.3 ( 0.0
> MIN)
> TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.84%
>
> --------------------------
> RHF SCF CALCULATION
> --------------------------
>
> NUCLEAR ENERGY = 2520.5794603055
> MAXIT = 199 NPUNCH= 2
> EXTRAP=T DAMP=T SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T
> DENSITY MATRIX CONV= 2.00E-05
> SOSCF WILL OPTIMIZE 16544 ORBITAL ROTATIONS, SOGTOL= 0.250
> MEMORY REQUIRED FOR RHF ITERS= 640658 WORDS.
>
> DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10
> SCHWARZ INEQUALITY OVERHEAD: 30854 INTEGRALS, T= 0.00
>
>
> NONZERO BLOCKS
> ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB.
> GRAD VIR. SHIFT DAMPING INTEGRALS SKIPPED
> 1 0 0 -2059.2212832191 -2059.2212832191 0.988797951
> 0.000000000 0.000000000 1.000000000 191835514 22895770
> 2 1 0 -2042.8253644320 16.3959187871 1.142306775
> 0.674963723 0.000000000 1.000000000 192284889 22920383
> 3 2 0 -2053.1297307637 -10.3043663316 0.401569267
> 0.408533345 0.000000000 54.508125229 192386468 22914751
> 4 3 0 -2054.8896748699 -1.7599441062 0.681705613
> 0.974133914 0.000000000 3.406757827 185808214 23658736
> ---------------START SECOND ORDER SCF---------------
> 5 4 0 -2060.2884381280 -5.3987632581 1.089757171
> 0.228307597 0.000000000 0.000000000 191024572 23175415
> 6 5 0 -2062.5678087125 -2.2793705845 0.335341404
> 0.164617327 0.000000000 0.000000000 191517675 23118064
> 7 6 0 -2063.0509541215 -0.4831454090 0.503307418
> 0.129756838 0.000000000 0.000000000 189580417 23389152
>
>
> I think the coords are the final config.
>
> Thanks for your help,
>
> Fred
>
> [32m*******************************************************************************
> Fred Dyda, Ph.D. Phone:301-402-4496
> Laboratory of Molecular Biology Fax: 301-496-0201
> DHHS/NIH/NIDDK e-mail:Fred.Dyda at nih.gov
> Bldg. 5. Room 303
> Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710 at mms.att.net
> Google maps coords: 39.000597, -77.102102
> http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
> *******************************************************************************
> [m
>
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