From owner-chemistry@ccl.net Sat Apr 8 00:24:01 2006 From: "Jonas Baltrusaitis jonas-baltrusaitis.:.uiowa.edu" To: CCL Subject: CCL:G: MOs are not on the checkpoint file error Message-Id: <-31456-060408002306-27347-Q/fVjLAIDRh+8aASj8CpcQ:_:server.ccl.net> X-Original-From: "Jonas Baltrusaitis" Date: Sat, 8 Apr 2006 00:23:02 -0400 Sent to CCL by: "Jonas Baltrusaitis" [jonas-baltrusaitis=uiowa.edu] Hi all, I am running Gaussia'98 on Linux cluster. No matter how my input looks like, I can't run multiple jobs with the following error: Leave Link 301 at Fri Apr 7 22:23:03 2006, MaxMem= 65536000 cpu: .1 (Enter /leu/g98/l401.exe) MOs are not on the checkpoint file. Error termination via Lnk1e in /leu/g98/l401.exe. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 5 Scr= 1 The input and output files are given below. thank You Jonas Baltrusaitis Input: %chk=AlO3NO3_mono_ONIOM.chk p opt oniom(hf/3-21g:pm3) nosymm guess=save geom=(connectivity) FChk=MO POP=FULL AlO3NO3 mono ONIOM -1 1 -1 1 Al 0 0.845462 1.794531 0.437739 H Al -1 1.918844 -1.180568 1.064343 L H 11 Al -1 -1.021469 1.991793 3.055598 L H 14 Al -1 3.361281 3.296027 1.769916 L H 13 Al -1 2.154461 0.824530 3.915976 L Al -1 4.021300 0.627240 1.298144 L O -1 3.702063 -1.115019 1.862533 L O -1 0.761750 2.057342 3.853788 L O -1 1.470808 -0.545798 2.860985 L O -1 3.369644 1.600202 2.744848 L O -1 2.238173 0.561719 0.499927 H O -1 4.013047 2.322999 0.323152 L O -1 1.529115 3.164858 1.492729 H O -1 -0.369703 1.018766 1.608834 H O -1 0.086678 -1.311736 0.787156 L O -1 -0.702121 3.733987 2.491149 L Al -1 1.081098 3.799536 3.289339 L Al -1 -0.361450 -0.676993 2.583825 L O -1 2.913264 3.930704 3.566526 L O -1 -1.013106 0.295969 4.030530 L O 0 0.193074 2.276925 -1.291361 H N 0 -0.289659 1.434557 -2.243719 H O 0 -0.468203 2.075876 -3.241342 H O 0 -0.518038 0.259577 -2.168386 H 1 11 1.0 13 1.0 14 1.0 21 1.0 2 7 1.0 9 1.0 11 1.0 15 1.0 3 8 1.0 14 1.0 16 1.0 20 1.0 4 10 1.0 12 1.0 13 1.0 19 1.0 5 8 1.0 9 1.0 10 1.0 6 7 1.0 10 1.0 11 1.0 12 1.0 7 8 17 1.0 9 18 1.0 10 11 12 13 17 1.0 14 18 1.0 15 18 1.0 16 17 1.0 17 19 1.0 18 20 1.0 19 20 21 22 1.0 22 23 2.0 24 2.0 23 24 --Link1-- %chk=AlO3NO3_mono_ONIOM.chk %nosave p opt=tight oniom(b3lyp/6-31+g(d):pm3) freq geom=allcheck guess=read AlNO3 mono ONIOM b3lyp -1 1 -1 1 Output: ......................................................................................... %chk=AlO3NO3_mono_ONIOM.chk %nosave Default route: MaxDisk=32GB --------------------------------------------------------------------- p opt=tight oniom(b3lyp/6-31+g(d):pm3) freq geom=allcheck guess=read --------------------------------------------------------------------- 1/7=10,14=-1,18=50,19=11,26=3,29=7,38=1,52=2/1,3; 2/9=110/2; 1/14=-1,18=50,19=11,38=1,52=2,53=92/20; 3/5=2,11=2,12=1,25=1,30=1/1; 4/5=1,11=1,20=7,22=1,24=1,35=1/1,2; 6/7=2,8=2,9=2,10=2/1; 7/7=1,33=-1/16; 1/14=-1,18=50,19=11,52=2,53=931/20; 3/5=1,6=6,7=11,11=2,25=1,30=1/1,2,3; 4/5=1/1; 5/5=2,42=-5,60=2/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=50,19=11,52=2,53=921/20; 3/5=2,11=2,12=1,25=1,30=1/1; 4/5=1,11=1,20=7,22=1,24=1,35=1/1,2; 6/7=2,8=2,9=2,10=2/1; 7/7=1,33=-1/16; 1/14=-1,18=50,19=11,52=2,53=315/20; 7/9=1,44=-1/16; 1/14=-1,18=50,19=11,52=2/3(1); 99//99; 2/9=110/2; 1/14=-1,18=50,19=11,52=2,53=392/20; 3/5=2,11=2,12=1,25=1,30=1/1; 4/5=5,11=1,16=2,20=7,22=1,24=1,35=1/1,2; 7/7=1,33=-1/16; 1/14=-1,18=50,19=11,52=2,53=231/20; 3/5=1,6=6,7=11,11=2,25=1,30=1/1,2,3; 4/5=5,16=2/1; 5/5=2,38=4,42=-5,60=2/2; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=50,19=11,52=2,53=121/20; 3/5=2,11=2,12=1,25=1,30=1/1; 4/5=5,11=1,16=2,20=7,22=1,24=1,35=1/1,2; 7/7=1,33=-1/16; 1/14=-1,18=50,19=11,52=2,53=315/20; 7/9=1,44=-1/16; 1/14=-1,18=50,19=11,52=2/3(-16); 2/9=110/2; 6/7=2,8=2,9=2,10=2/1; 99//99; Leave Link 1 at Fri Apr 7 22:23:01 2006, MaxMem= 0 cpu: .3 (Enter /leu/g98/l101.exe) ------------------ AlO3NO3 mono ONIOM ------------------ Redundant internal coordinates taken from checkpointfile: AlO3NO3_mono_ONIOM.chk Charge = -1 Multiplicity = 1 Charge = -1 Multiplicity = 1 in low level. Al,0,0.8808985156,1.771188424,0.5135092601 Al,0,1.9188440079,-1.1805679973,1.0643430127 Al,0,-1.0214689981,1.9917929974,3.0555980026 Al,0,3.3612810018,3.2960269962,1.76991599 Al,0,2.154461,0.82453,3.915976 Al,0,4.021299999,0.627240005,1.2981440019 O,0,3.7020629987,-1.1150189989,1.8625330028 O,0,0.7617500015,2.0573420003,3.8537880001 O,0,1.4708079982,-0.5457980009,2.8609849974 O,0,3.3696440002,1.6002020019,2.7448479998 O,0,2.2381729981,0.5617189441,0.4999269623 O,0,4.013047,2.3229989991,0.3231520006 O,0,1.5291149881,3.1648580483,1.4927290511 O,0,-0.3697029945,1.0187659989,1.6088339695 O,0,0.0866779989,-1.3117360001,0.7871559998 O,0,-0.7021210013,3.7339869992,2.4911489997 Al,0,1.0810980004,3.7995360011,3.2893389997 Al,0,-0.3614499988,-0.6769929942,2.58382501 O,0,2.913264,3.930704,3.566526 O,0,-1.013106,0.295969,4.03053 O,0,0.2386112117,2.404211929,-1.0651808735 N,0,0.0276023901,1.9288538936,-2.2990050768 O,0,-0.5186834354,2.6961398516,-3.1040867405 O,0,0.3923848771,0.7708250667,-2.5610815449 Fast transformation storage of 1 MWords has been initialized. Recover connectivity data from disk. Leave Link 101 at Fri Apr 7 22:23:01 2006, MaxMem= 65536000 cpu: .1 (Enter /leu/g98/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ------------------------ ------------------------- ! Name Definition Value Derivative Info. ! ----------------------------------------------------------------------------- ! X2 R(2,-1) 1.9188 Frozen ! ! Y2 R(2,-2) -1.1806 Frozen ! ! Z2 R(2,-3) 1.0643 Frozen ! ! X3 R(3,-1) -1.0215 Frozen ! ! Y3 R(3,-2) 1.9918 Frozen ! ! Z3 R(3,-3) 3.0556 Frozen ! ! X4 R(4,-1) 3.3613 Frozen ! ! Y4 R(4,-2) 3.296 Frozen ! ! Z4 R(4,-3) 1.7699 Frozen ! ! X5 R(5,-1) 2.1545 Frozen ! ! Y5 R(5,-2) 0.8245 Frozen ! ! Z5 R(5,-3) 3.916 Frozen ! ! X6 R(6,-1) 4.0213 Frozen ! ! Y6 R(6,-2) 0.6272 Frozen ! ! Z6 R(6,-3) 1.2981 Frozen ! ! X7 R(7,-1) 3.7021 Frozen ! ! Y7 R(7,-2) -1.115 Frozen ! ! Z7 R(7,-3) 1.8625 Frozen ! ! X8 R(8,-1) 0.7618 Frozen ! ! Y8 R(8,-2) 2.0573 Frozen ! ! Z8 R(8,-3) 3.8538 Frozen ! ! X9 R(9,-1) 1.4708 Frozen ! ! Y9 R(9,-2) -0.5458 Frozen ! ! Z9 R(9,-3) 2.861 Frozen ! ! X10 R(10,-1) 3.3696 Frozen ! ! Y10 R(10,-2) 1.6002 Frozen ! ! Z10 R(10,-3) 2.7448 Frozen ! ! X11 R(11,-1) 2.2382 Frozen ! ! Y11 R(11,-2) 0.5617 Frozen ! ! Z11 R(11,-3) 0.4999 Frozen ! ! X12 R(12,-1) 4.013 Frozen ! ! Y12 R(12,-2) 2.323 Frozen ! ! Z12 R(12,-3) 0.3232 Frozen ! ! X13 R(13,-1) 1.5291 Frozen ! ! Y13 R(13,-2) 3.1649 Frozen ! ! Z13 R(13,-3) 1.4927 Frozen ! ! X14 R(14,-1) -0.3697 Frozen ! ! Y14 R(14,-2) 1.0188 Frozen ! ! Z14 R(14,-3) 1.6088 Frozen ! ! X15 R(15,-1) 0.0867 Frozen ! ! Y15 R(15,-2) -1.3117 Frozen ! ! Z15 R(15,-3) 0.7872 Frozen ! ! X16 R(16,-1) -0.7021 Frozen ! ! Y16 R(16,-2) 3.734 Frozen ! ! Z16 R(16,-3) 2.4911 Frozen ! ! X17 R(17,-1) 1.0811 Frozen ! ! Y17 R(17,-2) 3.7995 Frozen ! ! Z17 R(17,-3) 3.2893 Frozen ! ! X18 R(18,-1) -0.3614 Frozen ! ! Y18 R(18,-2) -0.677 Frozen ! ! Z18 R(18,-3) 2.5838 Frozen ! ! X19 R(19,-1) 2.9133 Frozen ! ! Y19 R(19,-2) 3.9307 Frozen ! ! Z19 R(19,-3) 3.5665 Frozen ! ! X20 R(20,-1) -1.0131 Frozen ! ! Y20 R(20,-2) 0.296 Frozen ! ! Z20 R(20,-3) 4.0305 Frozen ! ! R1 R(1,11) 1.818 estimate D2E/DX2 ! ! R2 R(1,13) 1.8225 estimate D2E/DX2 ! ! R3 R(1,14) 1.8248 estimate D2E/DX2 ! ! R4 R(1,21) 1.8181 estimate D2E/DX2 ! ! R5 R(21,22) 1.339 estimate D2E/DX2 ! ! R6 R(22,23) 1.2391 estimate D2E/DX2 ! ! R7 R(22,24) 1.2421 estimate D2E/DX2 ! ! A1 A(11,1,13) 104.3128 estimate D2E/DX2 ! ! A2 A(11,1,14) 103.9942 estimate D2E/DX2 ! ! A3 A(11,1,21) 119.2674 estimate D2E/DX2 ! ! A4 A(13,1,14) 103.6839 estimate D2E/DX2 ! ! A5 A(13,1,21) 109.0229 estimate D2E/DX2 ! ! A6 A(14,1,21) 115.0024 estimate D2E/DX2 ! ! A7 A(1,11,2) 119.5363 estimate D2E/DX2 ! ! A8 A(1,11,6) 130.9709 estimate D2E/DX2 ! ! A9 A(1,13,4) 119.0106 estimate D2E/DX2 ! ! A10 A(1,13,17) 131.2786 estimate D2E/DX2 ! ! A11 A(1,14,3) 119.4045 estimate D2E/DX2 ! ! A12 A(1,14,18) 130.825 estimate D2E/DX2 ! ! A13 A(1,21,22) 137.071 estimate D2E/DX2 ! ! A14 A(21,22,23) 116.6386 estimate D2E/DX2 ! ! A15 A(21,22,24) 118.6293 estimate D2E/DX2 ! ! A16 A(23,22,24) 124.7306 estimate D2E/DX2 ! ! D1 D(13,1,11,2) 125.7697 estimate D2E/DX2 ! ! D2 D(13,1,11,6) -0.3631 estimate D2E/DX2 ! ! D3 D(14,1,11,2) 17.3971 estimate D2E/DX2 ! ! D4 D(11,1,13,4) 17.5082 estimate D2E/DX2 ! ! D5 D(11,1,13,17) -108.4418 estimate D2E/DX2 ! ! D6 D(14,1,13,4) 126.1095 estimate D2E/DX2 ! ! D7 D(11,1,14,3) 125.9491 estimate D2E/DX2 ! ! D8 D(11,1,14,18) -0.1293 estimate D2E/DX2 ! ! D9 D(13,1,14,3) 17.1107 estimate D2E/DX2 ! ! D10 D(11,1,21,22) 35.5548 estimate D2E/DX2 ! ! D11 D(13,1,21,22) 155.0915 estimate D2E/DX2 ! ! D12 D(7,2,11,1) -142.3346 estimate D2E/DX2 ! ! D13 D(9,2,11,1) -62.5961 estimate D2E/DX2 ! ! D14 D(8,3,14,1) -62.552 estimate D2E/DX2 ! ! D15 D(16,3,14,1) 23.8738 estimate D2E/DX2 ! ! D16 D(10,4,13,1) -62.6242 estimate D2E/DX2 ! ! D17 D(12,4,13,1) 23.6384 estimate D2E/DX2 ! ! D18 D(7,6,11,1) 135.2413 estimate D2E/DX2 ! ! D19 D(10,6,11,1) 34.0994 estimate D2E/DX2 ! ! D20 D(1,13,17,8) 33.8649 estimate D2E/DX2 ! ! D21 D(1,13,17,16) -52.2517 estimate D2E/DX2 ! ! D22 D(1,14,18,9) 34.0583 estimate D2E/DX2 ! ! D23 D(1,14,18,15) -51.9227 estimate D2E/DX2 ! ! D24 D(1,21,22,23) 175.9145 estimate D2E/DX2 ! ! D25 D(1,21,22,24) -4.4972 estimate D2E/DX2 ! ----------------------------------------------------------------------------- Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-06 Number of steps in this run= 115 maximum allowed number of steps= 144. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Leave Link 103 at Fri Apr 7 22:23:02 2006, MaxMem= 65536000 cpu: .1 (Enter /leu/g98/l202.exe) Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 13 0 .880899 1.771188 .513509 2 13 0 1.918844 -1.180568 1.064343 3 13 0 -1.021469 1.991793 3.055598 4 13 0 3.361281 3.296027 1.769916 5 13 0 2.154461 .824530 3.915976 6 13 0 4.021300 .627240 1.298144 7 8 0 3.702063 -1.115019 1.862533 8 8 0 .761750 2.057342 3.853788 9 8 0 1.470808 -.545798 2.860985 10 8 0 3.369644 1.600202 2.744848 11 8 0 2.238173 .561719 .499927 12 8 0 4.013047 2.322999 .323152 13 8 0 1.529115 3.164858 1.492729 14 8 0 -.369703 1.018766 1.608834 15 8 0 .086678 -1.311736 .787156 16 8 0 -.702121 3.733987 2.491149 17 13 0 1.081098 3.799536 3.289339 18 13 0 -.361450 -.676993 2.583825 19 8 0 2.913264 3.930704 3.566526 20 8 0 -1.013106 .295969 4.030530 21 8 0 .238611 2.404212 -1.065181 22 7 0 .027602 1.928854 -2.299005 23 8 0 -.518683 2.696140 -3.104087 24 8 0 .392385 .770825 -2.561082 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 Al .000000 2 Al 3.177045 .000000 3 Al 3.182748 4.761766 .000000 4 Al 3.171118 4.755876 4.750000 .000000 5 Al 3.754318 3.493958 3.491316 3.488594 .000000 6 Al 3.433131 2.782652 5.511821 2.789376 3.221344 7 O 4.255470 1.954808 5.778187 4.425160 3.220800 8 O 3.354630 4.427633 1.954808 3.554494 1.861004 9 O 3.350681 1.957445 3.562118 4.418590 1.859620 10 O 3.346933 3.558314 4.419478 1.956115 1.857385 11 O 1.818020 1.859059 4.381990 3.217248 3.427166 12 O 3.186077 4.148498 5.737797 1.861373 4.313715 13 O 1.822463 4.383849 3.213117 1.857652 3.426415 14 O 1.824796 3.220402 1.861372 4.374026 3.425206 15 O 3.195323 1.857652 4.157779 5.737623 4.316118 16 O 3.204620 5.749616 1.858985 4.150087 4.319159 17 Al 3.443763 5.518502 2.782689 2.785929 3.224196 18 Al 3.438492 2.786064 2.789375 5.505094 3.218541 19 O 4.256164 5.777101 4.416169 1.957381 3.216553 20 O 4.258281 4.424337 1.956114 5.765933 3.213406 21 O 1.818107 4.495409 4.328823 4.310937 5.565770 22 N 2.943333 4.955543 5.456765 5.434951 6.661010 23 O 3.987652 6.192432 6.220178 6.258585 7.741441 24 O 3.269936 4.391095 5.919192 5.826537 6.712680 6 7 8 9 10 6 Al .000000 7 O 1.859009 .000000 8 O 4.381914 4.761766 .000000 9 O 3.213020 2.509864 2.874849 .000000 10 O 1.861253 2.874266 2.870511 2.867818 .000000 11 O 1.954734 2.609812 3.957916 2.718462 2.719990 12 O 1.956087 3.779732 4.806963 4.597126 2.607875 13 O 3.562072 4.814126 2.718463 3.955312 2.720937 14 O 4.419358 4.603985 2.720045 2.720887 3.951115 15 O 4.416105 3.777055 4.605501 2.608303 4.805185 16 O 5.778048 6.580642 2.609759 4.814038 4.603984 17 Al 4.761629 5.749616 1.858985 4.383753 3.220401 18 Al 4.750000 4.150213 3.217293 1.857740 4.374084 19 O 4.157665 5.383783 2.867232 4.755790 2.512902 20 O 5.737675 5.378096 2.506748 2.871626 4.750000 21 O 4.801215 5.740383 4.958855 5.063166 4.996611 22 N 5.530217 6.331289 6.197769 5.901885 6.059514 23 O 6.653678 7.550294 7.103492 7.074625 7.108460 24 O 5.299364 5.837700 6.553023 5.682895 6.140426 11 12 13 14 15 11 O .000000 12 O 2.506698 .000000 13 O 2.874848 2.871682 .000000 14 O 2.870468 4.750000 2.867874 .000000 15 O 2.867275 5.370565 4.755876 2.512902 .000000 16 O 4.761678 5.378095 2.509814 2.874266 5.383783 17 Al 4.427539 4.424336 1.957382 3.558315 5.777101 18 Al 3.554585 5.766005 4.418659 1.956086 1.957482 19 O 4.605414 3.783347 2.608260 4.805186 6.572493 20 O 4.806932 6.566256 4.597156 2.607875 3.783347 21 O 3.137290 4.022490 2.964268 3.072436 4.154817 22 N 3.819647 4.786943 4.261396 4.032036 4.475411 23 O 5.014472 5.694013 5.054096 5.004738 5.618835 24 O 3.580563 4.882340 4.843235 4.246228 3.954897 16 17 18 19 20 16 O .000000 17 Al 1.954808 .000000 18 Al 4.425086 4.755839 .000000 19 O 3.777055 1.857652 5.737624 .000000 20 O 3.779732 4.148498 1.861254 5.370566 .000000 21 O 3.911619 4.649576 4.813433 5.562073 5.654888 22 N 5.170742 5.986559 5.548318 6.836586 6.619094 23 O 5.693631 6.682266 6.614763 7.602597 7.543741 24 O 5.958465 6.623808 5.397639 7.340793 6.756496 21 22 23 24 21 O .000000 22 N 1.338959 .000000 23 O 2.194505 1.239077 .000000 24 O 2.220207 1.242087 2.198121 .000000 Stoichiometry Al8NO15(1-) Framework group C1[X(Al8NO15)] Deg. of freedom 66 Full point group C1 NOp 1 Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 13 0 1.122335 -.452583 -.092453 2 13 0 .493261 2.583041 .602436 3 13 0 -.863594 -1.753121 2.027587 4 13 0 -.804607 -.684468 -2.600264 5 13 0 -2.433027 .730481 .141351 6 13 0 -.366261 1.999269 -1.978957 7 8 0 -.732737 3.324242 -.727535 8 8 0 -2.089592 -1.011919 .697616 9 8 0 -1.164135 1.677435 1.116737 10 8 0 -1.653124 .726725 -1.544358 11 8 0 .859739 1.258090 -.649083 12 8 0 .482290 .588191 -3.034938 13 8 0 -.065717 -1.431264 -1.068203 14 8 0 .423303 -.480462 1.592912 15 8 0 1.232151 1.836245 2.134495 16 8 0 -.497085 -3.077979 .776089 17 13 0 -1.723083 -2.336777 -.553882 18 13 0 -.425247 .930616 2.648893 19 8 0 -2.461973 -1.589981 -2.085941 20 8 0 -1.712111 -.341928 3.083493 21 8 0 2.774094 -1.195455 -.251655 22 7 0 4.045816 -.788873 -.150532 23 8 0 4.918588 -1.661139 -.263377 24 8 0 4.271582 .417720 .039057 --------------------------------------------------------------------- Rotational constants (GHZ): .2092432 .1746905 .1739013 Isotopes: Al-27,Al-27,Al-27,Al-27,Al-27,Al-27,O-16,O-16,O-16,O-16,O-16,O-16,O-16 ,O-16,O-16,O-16,Al-27,Al-27,O-16,O-16,O-16,N-14,O-16,O-16 Leave Link 202 at Fri Apr 7 22:23:02 2006, MaxMem= 65536000 cpu: .1 (Enter /leu/g98/l120.exe) ONIOM: Cut between Al/H 2 and O 11 factor= .497426 ONIOM: Cut between Al/H 3 and O 14 factor= .497426 ONIOM: Cut between Al/H 4 and O 13 factor= .497426 ONIOM: generating new system at layer 2 ONIOM: saving gridpoint 9 Leave Link 120 at Fri Apr 7 22:23:03 2006, MaxMem= 65536000 cpu: .0 (Enter /leu/g98/l301.exe) Standard basis: VSTO-3G (5D, 7F) There are 96 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 96 basis functions 288 primitive gaussians 60 alpha electrons 60 beta electrons nuclear repulsion energy 995.6799861472 Hartrees. Leave Link 301 at Fri Apr 7 22:23:03 2006, MaxMem= 65536000 cpu: .1 (Enter /leu/g98/l401.exe) MOs are not on the checkpoint file. Error termination via Lnk1e in /leu/g98/l401.exe. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. From owner-chemistry@ccl.net Sat Apr 8 00:58:04 2006 From: "Jason Stephen D Acchioli jsd44 a cornell.edu" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-31457-060408003235-31356-O22h6vxy8zCQ9miA47XvhA*_*server.ccl.net> X-Original-From: "Jason Stephen D Acchioli" Date: Sat, 8 Apr 2006 00:32:33 -0400 Sent to CCL by: "Jason Stephen D Acchioli" [jsd44 . cornell.edu] Hi all, I was wondering if anyone knew how to visualize the NBO 3.1 orbitals produced by Gaussian 03. I don't have access to NBO 5.0. I've tried using some functions in Molekel to do it, but to no avail. If someone has a method, complete with instructions, it would be greatly appreciated! Be well, Jason From owner-chemistry@ccl.net Sat Apr 8 09:10:01 2006 From: "Hajime Ohno h_ohno(-)cheng.es.osaka-u.ac.jp" To: CCL Subject: CCL: Total charge of whole protein Message-Id: <-31458-060408033706-1327-MlhDo5MgI87aOVuibu+VxA+*+server.ccl.net> X-Original-From: "Hajime Ohno" Date: Sat, 8 Apr 2006 03:37:02 -0400 Sent to CCL by: "Hajime Ohno" [h_ohno{}cheng.es.osaka-u.ac.jp] Hello. I am a student of Osaka university in Japan and studying a redox reaction in a protein (PDB: 1B4V) by the QM/MM approach to compute free energy change. It can be easily expected that the total charge of the protein affects seriously the redox potential. My question is how I can get the proper value of the total charge of the whole protein. In other words, how can we know the protnation states of the constituent amino acids in the protein? At present, we fully rely on the web tool MOLPROBITY to add hydrogen atoms on the PDB data. If it cant be known at all, how do researchers who study protein deal with the problem? Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531, Japan Hajime Ohno e-mail: h_ohno(a)cheng.es.osaka-u.ac.jp From owner-chemistry@ccl.net Sat Apr 8 09:45:01 2006 From: "Kirkpatrick, James james.kirkpatrick^-^imperial.ac.uk" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-31459-060408003235-12345-mMnVujfAs4yG9gkINI2NuQ_+_server.ccl.net> X-Original-From: "Kirkpatrick, James" Date: Sat, 8 Apr 2006 11:36:43 +0100 Sent to CCL by: "Kirkpatrick, James" [james.kirkpatrick+/-imperial.ac.uk] [winmail.dat attachment removed by CCL Admin] Hi Jason, what you could do is use the SaveNBOs to save the orbitals to checkpoint file, then visualise them with gaussview. If this is not avalable you can generate cube file using the cubegen command ( http://www.gaussian.com/g_ur/u_cubegen.htm ), then visualise the cube file with a program such as Molden ( http://www.cmbi.ru.nl/molden/molden.html ), maybe Molekel can do it too? I have never worked with NBO, but this is my tuppence! James -----Original Message----- From: Jason Stephen D Acchioli jsd44 a cornell.edu = [mailto:owner-chemistry|,|ccl.net] Sent: Sat 08/04/2006 06:38 To: Kirkpatrick, James Subject: CCL:G: NBO visualization Sent to CCL by: "Jason Stephen D Acchioli" [jsd44 . cornell.edu] Hi all, I was wondering if anyone knew how to visualize the NBO 3.1 orbitals produced by Gaussian 03. I don't have access to NBO 5.0. I've tried using some functions in Molekel to do it, but to no avail. If someone has a method, complete with instructions, it would be greatly appreciated! Be well, Jason From owner-chemistry@ccl.net Sat Apr 8 22:18:00 2006 From: "Dr. N. SUKUMAR nagams-#-rpi.edu" To: CCL Subject: CCL: Total charge of whole protein Message-Id: <-31460-060408113534-644-qvzLbBg9RPrVNXllbakG3w.:.server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sat, 08 Apr 2006 11:35:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams]![rpi.edu] ==============Original message text=============== On Sat, 08 Apr 2006 9:15:46 EDT "Hajime Ohno h_ohno(-)cheng.es.osaka-u.ac.jp" wrote: Sent to CCL by: "Hajime Ohno" [h_ohno{}cheng.es.osaka-u.ac.jp] Hello. I am a student of Osaka university in Japan and studying a redox reaction in a protein (PDB: 1B4V) by the QM/MM approach to compute free energy change. It can be easily expected that the total charge of the protein affects seriously the redox potential. My question is how I can get the proper value of the total charge of the whole protein. In other words, how can we know the protnation states of the constituent amino acids in the protein? At present, we fully rely on the web tool MOLPROBITY to add hydrogen atoms on the PDB data. If it cant be known at all, how do researchers who study protein deal with the problem? Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531, Japan Hajime Ohno e-mail: h_ohno=cheng.es.osaka-u.ac.jp ===========End of original message text=========== There are several tools that do this. A few of them are: * PROPKA webserver from Jensen (Iowa) - http://propka.chem.uiowa.edu/Fast empirical method for structure-based protein pKa prediction and rationalization. Desolvation effects and intra-protein interactions causing variations in pKa values of protein ionizable groups are empirically related to the positions and identities of the groups proximate to the pKa sites. * WHAT IF - Finite Difference (FDPB) / Analytical Poisson Boltzmann Solver from Vriend (Netherlands) & Nielsen (EMBL) http://enzyme.ucd.ie/Science/pKa/Calculates (1) desolvation energy (Born energy) associated with moving the neutral and charged form of the group from to its present position in the protein, (2) background interaction energies of the neutral and charged form of the residue with the permanent dipoles of the protein, (3) (pair wise) interaction energies between titratable groups. * MM_SCP - Micro-environment Modulated Screened Coulomb Potential from E.L. Mehler (Mt. Sinai) - http://fulcrum.physbio.mssm.edu/~mehler/text/pka.htmlAssumes that hydrophobicity/hydrophilicity of residues/fragments near the given titratable group is the relevant quantity for characterizing the local microenvironment. Rekker Fragmental Hydrophobic Constants (fitted lo logPo/w) employed to evaluate hydrophobicities of the microenvironments. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute