<div dir="ltr">Fred<div><br></div><div>The GAMESS run has failed. It should have something like</div><div><br></div><div>
<p class=""><span class=""> ***** EQUILIBRIUM GEOMETRY LOCATED *****</span></p>
<p class=""><span class=""> COORDINATES OF ALL ATOMS ARE (ANGS)</span></p>
<p class=""><span class=""> ATOM CHARGE X Y Z</span></p>
<p class=""><span class=""> ------------------------------------------------------------</span></p>
<p class=""><span class=""> CR 24.0 -1.4046704720 -0.0044107654 -0.4346577152</span></p>
<p class=""><span class=""> O 8.0 0.3767999588 -0.0356515989 -0.1243040639</span></p>
<p class=""><span class=""> H 1.0 1.1070887248 -0.0807544290 0.4885987331</span></p>
<p class=""><span class=""></span>and end with</p><p class=""><span class="">......END OF GEOMETRY SEARCH......</span></p><p class=""><span class=""> STEP CPU TIME = 0.00 TOTAL CPU TIME = 13.0 ( 0.2 MIN)</span></p><p class=""><span class=""> TOTAL WALL CLOCK TIME= 16.0 SECONDS, CPU UTILIZATION IS 81.31%</span></p><p class=""><span class=""> 1046951 WORDS OF DYNAMIC MEMORY USED</span></p><p class=""><span class=""> EXECUTION OF GAMESS TERMINATED NORMALLY Tue Mar 1 11:03:46 2016</span></p><p class=""><span class=""> DDI: 262808 bytes (0.3 MB / 0 MWords) used by master data server.</span></p><p class=""><span class=""></span><br></p><p class=""><span class=""> ----------------------------------------</span></p><p class=""><span class=""> CPU timing information for all processes</span></p><p class=""><span class=""> ========================================</span></p><p class=""><span class=""> 0: 12.777090 + 0.248382 = 13.025472</span></p><p class=""><span class=""> 1: 0.001435 + 0.002468 = 0.003903</span></p><p class=""><span class=""> ----------------------------------------</span></p><p class="">
</p><p class=""><span class=""> ddikick.x: exited gracefully.</span></p><p class=""><span class=""><br></span></p><p class=""><span class="">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.</span></p></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 1, 2016 at 2:54 PM, Dyda <span dir="ltr"><<a href="mailto:dyda@ulti.niddk.nih.gov" target="_blank">dyda@ulti.niddk.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Nigel,<br>
<br>
I agree, but pdb is what I have. I should think that the quality of the input should not<br>
impact whether .cif is output or not.<br>
<br>
The end of .gam:<br>
<br>
COORDINATES OF ALL ATOMS ARE (ANGS)<br>
ATOM CHARGE X Y Z<br>
------------------------------------------------------------<br>
CR 24.0 0.<a href="tel:1912339815%20%20-0" value="+19123398150">1912339815 -0</a>.0759848760 -0.0714344444<br>
O 8.0 2.3234578345 -0.2357845497 -0.1508067587<br>
O 8.0 -0.7105232282 0.0098034893 1.8036685126<br>
O 8.0 1.2076867850 -0.3346443692 -1.7335283981<br>
O 8.0 -0.5260639033 1.7906968578 0.3539796904<br>
O 8.0 0.9068338690 -1.9599479901 -0.6296444533<br>
O 8.0 -1.9397708185 -0.1141525894 0.1891144601<br>
C 6.0 2.8515146213 -0.0055174102 1.1989521238<br>
C 6.0 1.9707450903 -0.6979131843 2.5449414024<br>
C 6.0 0.4359449408 -0.0451724719 2.8465226464<br>
C 6.0 3.0118766316 1.4363395032 1.6481146467<br>
C 6.0 -0.0653144611 0.1564048347 4.4949200023<br>
C 6.0 0.6249516515 0.4233319450 -2.8992641137<br>
C 6.0 0.1643384668 2.4470081023 -2.2535061934<br>
C 6.0 -0.9128640701 2.5088690737 -0.8469830060<br>
C 6.0 1.5743374229 0.5462852223 -3.8500329514<br>
C 6.0 -1.2118325877 3.9283584299 -0.4940679455<br>
C 6.0 -0.1968029455 -3.0386081819 -0.8007813286<br>
C 6.0 -1.6882650231 -2.4665688184 -1.2935287464<br>
C 6.0 -2.6276161825 -1.2806785380 -0.2996777905<br>
C 6.0 -0.3391479898 -3.6453123923 0.6022767778<br>
C 6.0 -4.1453203443 -1.5862494692 0.1854244826<br>
H 1.0 3.8553615186 -0.4420315035 1.2332199192<br>
H 1.0 2.2818981212 -1.6647647766 3.1911897462<br>
H 1.0 1.9667722755 1.9810594320 1.6970399031<br>
H 1.0 3.6823942975 1.6618943249 2.5365171626<br>
H 1.0 3.6238703905 1.9113333115 0.7438740891<br>
H 1.0 0.8971167594 0.4695270592 5.1329947121<br>
H 1.0 -0.6645891831 1.2206664940 4.5846682936<br>
H 1.0 -0.6246971002 -0.6219821332 4.8583146656<br>
H 1.0 -0.2487681929 -0.1134304045 -3.2439960069<br>
H 1.0 1.1860397915 3.0186834522 -2.1641816248<br>
H 1.0 -0.3750591440 2.8925729326 -3.2804399647<br>
H 1.0 -1.9371292026 2.0739333624 -1.0806155814<br>
H 1.0 1.9496290579 -0.6216286700 -4.2730835081<br>
H 1.0 2.4497745286 1.0199721671 -3.6228827183<br>
H 1.0 1.0277269687 0.9853088788 -4.8324755816<br>
H 1.0 -1.6488875565 4.5338413808 -1.4704889855<br>
H 1.0 -1.7951603842 3.9656768136 0.3514485986<br>
H 1.0 -0.2983062508 4.5239905524 -0.4318350930<br>
H 1.0 0.1219656972 -3.8775516930 -1.5693737575<br>
H 1.0 -2.2141859609 -2.6816187114 -2.2405875656<br>
H 1.0 0.7133579392 -3.9124935444 1.0380228614<br>
H 1.0 -0.7783653014 -2.9666445248 1.3120392457<br>
H 1.0 -0.9150821609 -4.6238970562 0.5814496583<br>
H 1.0 -4.2320258907 -2.8021018481 0.2370382406<br>
H 1.0 -4.7833967302 -1.1881592471 -0.7055025179<br>
H 1.0 -4.4126745266 -1.1246420328 1.0220077683<br>
<br>
********************<br>
1 ELECTRON INTEGRALS<br>
********************<br>
...... END OF ONE-ELECTRON INTEGRALS ......<br>
CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0 MIN)<br>
TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 100.00%<br>
<br>
-------------<br>
GUESS OPTIONS<br>
-------------<br>
GUESS =HUCKEL NORB = 0 NORDER= 0<br>
MIX = F PRTMO = F PUNMO = F<br>
TOLZ = 1.0E-08 TOLE = 1.0E-05<br>
SYMDEN= F PURIFY= F<br>
<br>
INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.<br>
HUCKEL GUESS REQUIRES 649929 WORDS.<br>
<br>
SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S).<br>
94 ORBITALS ARE OCCUPIED ( 30 CORE ORBITALS).<br>
31=A 32=A 33=A 34=A 35=A 36=A 37=A<br>
38=A 39=A 40=A 41=A 42=A 43=A 44=A<br>
45=A 46=A 47=A 48=A 49=A 50=A 51=A<br>
52=A 53=A 54=A 55=A 56=A 57=A 58=A<br>
59=A 60=A 61=A 62=A 63=A 64=A 65=A<br>
66=A 67=A 68=A 69=A 70=A 71=A 72=A<br>
73=A 74=A 75=A 76=A 77=A 78=A 79=A<br>
80=A 81=A 82=A 83=A 84=A 85=A 86=A<br>
87=A 88=A 89=A 90=A 91=A 92=A 93=A<br>
94=A 95=A 96=A 97=A 98=A 99=A 100=A<br>
101=A 102=A 103=A 104=A<br>
...... END OF INITIAL ORBITAL SELECTION ......<br>
CPU 0: STEP CPU TIME= 0.24 TOTAL CPU TIME= 0.3 ( 0.0 MIN)<br>
TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.49%<br>
<br>
----------------------<br>
AO INTEGRAL TECHNOLOGY<br>
----------------------<br>
S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY<br>
KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR).<br>
S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY<br>
KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE).<br>
S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5,<br>
ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED<br>
SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER).<br>
S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY<br>
MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY).<br>
<br>
--------------------<br>
2 ELECTRON INTEGRALS<br>
--------------------<br>
<br>
DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK.<br>
DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK.<br>
...... END OF TWO-ELECTRON INTEGRALS .....<br>
CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 0.3 ( 0.0 MIN)<br>
TOTAL WALL CLOCK TIME= 0.4 SECONDS, CPU UTILIZATION IS 86.84%<br>
<br>
--------------------------<br>
RHF SCF CALCULATION<br>
--------------------------<br>
<br>
NUCLEAR ENERGY = 2520.5794603055<br>
MAXIT = 199 NPUNCH= 2<br>
EXTRAP=T DAMP=T SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T<br>
DENSITY MATRIX CONV= 2.00E-05<br>
SOSCF WILL OPTIMIZE 16544 ORBITAL ROTATIONS, SOGTOL= 0.250<br>
MEMORY REQUIRED FOR RHF ITERS= 640658 WORDS.<br>
<br>
DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10<br>
SCHWARZ INEQUALITY OVERHEAD: 30854 INTEGRALS, T= 0.00<br>
<br>
NONZERO BLOCKS<br>
ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD VIR. SHIFT DAMPING INTEGRALS SKIPPED<br>
1 0 0 -2059.2212832191 -2059.2212832191 0.988797951 0.000000000 0.000000000 1.000000000 191835514 22895770<br>
2 1 0 -2042.8253644320 16.3959187871 1.142306775 0.674963723 0.000000000 1.000000000 192284889 22920383<br>
3 2 0 -2053.1297307637 -10.3043663316 0.401569267 0.408533345 0.000000000 54.508125229 192386468 22914751<br>
4 3 0 -2054.8896748699 -1.7599441062 0.681705613 0.974133914 0.000000000 3.406757827 185808214 23658736<br>
---------------START SECOND ORDER SCF---------------<br>
5 4 0 -2060.2884381280 -5.3987632581 1.089757171 0.228307597 0.000000000 0.000000000 191024572 23175415<br>
6 5 0 -2062.5678087125 -2.2793705845 0.335341404 0.164617327 0.000000000 0.000000000 191517675 23118064<br>
7 6 0 -2063.0509541215 -0.4831454090 0.503307418 0.129756838 0.000000000 0.000000000 189580417 23389152<br>
<br>
<br>
I think the coords are the final config.<br>
<br>
Thanks for your help,<br>
<br>
Fred<br>
[32m*******************************************************************************<br>
Fred Dyda, Ph.D. Phone:301-402-4496<br>
Laboratory of Molecular Biology Fax: 301-496-0201<br>
DHHS/NIH/NIDDK <a href="mailto:e-mail%3AFred.Dyda@nih.gov">e-mail:Fred.Dyda@nih.gov</a><br>
Bldg. 5. Room 303<br>
Bethesda, MD 20892-0560 URGENT message e-mail: <a href="mailto:2022476710@mms.att.net">2022476710@mms.att.net</a><br>
Google maps coords: 39.000597, -77.102102<br>
<a href="http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred" rel="noreferrer" target="_blank">http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred</a><br>
******************************************************************************* [m<br>
</blockquote></div><br></div>