[phenixbb] phenix.elbow with GAMESS
Dyda
dyda at ulti.niddk.nih.gov
Tue Mar 1 14:54:30 PST 2016
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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