Mon Oct 10 20:16:59 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 20:16:59 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIR 239 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6153952 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -10.43000 40.31400 ymin,ymax (A): 33.39800 88.76300 zmin,zma (A): -12.35300 45.49600 x,y,z range (A): 50.74400 55.36500 57.84900 scale (grids/A): 0.6153952 object centre (A): 14.94200 61.08050 16.57150 number of atom coordinates read : 2578 total number of charged atoms : 2442 net assigned charge : -0.9859928 assigned positive charge : 383.8508 centred at (gu) : 90.64661 88.25932 90.07526 assigned negative charge : -384.8379 centred at (gu) : 90.59663 88.39548 90.08416 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6629 nv = 96 ne = 84 npr = 51235 no. pairs analyzed = 51235 no. exposed pairs = 3632 no. arc points = 25662 no. surface atoms = 1200 nbur = 1378 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3238 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3200000 number of dielectric boundary points 3721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2540 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3816761E-10 -1.3880703E-09 midg,1,midg; midg,igrid,midg 1.0212402E-08 -5.9671432E-09 1,midg,midg; igrid,midg,midg -3.2389322E-09 2.3240345E-09 gauss-seidel spectral radius is 0.9863380 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 20:17:00 rms-change max change #iterations 0.1166288 19.07737 at 10iterations 1.0613313E-02 1.693466 at 20iterations 9.6084567E-04 0.1488533 at 30iterations 9.5744916E-05 1.8989563E-02 at 40iterations 1.2426430E-05 2.1839142E-03 at 50iterations finished qdiffx linear iterations at : 20:17:02 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.2426430E-05 2.1839142E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 20:17:03 3.160u 0.164s 0:03.89 85.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 20:17:03 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIR 239 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.846186 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -10.43000 40.31400 ymin,ymax (A): 33.39800 88.76300 zmin,zma (A): -12.35300 45.49600 x,y,z range (A): 50.74400 55.36500 57.84900 scale (grids/A): 1.846186 object centre (A): 14.94200 61.08050 16.57150 number of atom coordinates read : 2578 total number of charged atoms : 2442 net assigned charge : -0.9859928 assigned positive charge : 383.8508 centred at (gu) : 91.93927 84.77692 90.22498 assigned negative charge : -384.8379 centred at (gu) : 91.79003 85.18655 90.25239 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 24592 mr = 45732 m= 4015 mr = 17123 m= 197 mr = 2213 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 396 time to turn everything in is 0.4900000 number of dielectric boundary points 34210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19154 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6153952 object centre at (A) : 14.94200 61.08050 16.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5254276E-03 -3.4182701E-02 midg,1,midg; midg,igrid,midg 5.5712849E-02 -1.2767101E-02 1,midg,midg; igrid,midg,midg -2.8457870E-03 -5.1210080E-03 gauss-seidel spectral radius is 0.9985660 estimated iterations to convergence 209 setup time was (sec) 0.7500000 now iterating at: 20:17:04 rms-change max change #iterations 3.934579 160.5861 at 10iterations 1.795489 79.73357 at 20iterations 0.8205107 28.43739 at 30iterations 0.3766185 13.40335 at 40iterations 0.1723545 5.762400 at 50iterations 7.9180986E-02 2.499924 at 60iterations 3.6314879E-02 1.192837 at 70iterations 1.6572803E-02 0.6036396 at 80iterations 7.6141641E-03 0.2604904 at 90iterations 3.5084886E-03 0.1134514 at 100iterations 1.6098368E-03 6.1341286E-02 at 110iterations 7.4342103E-04 2.5476456E-02 at 120iterations finished qdiffx linear iterations at : 20:17:10 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 7.4342103E-04 2.5476456E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 20:17:11 6.881u 0.169s 0:07.93 88.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 20:17:11 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIR 239 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.769279 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -10.43000 40.31400 ymin,ymax (A): 33.39800 88.76300 zmin,zma (A): -12.35300 45.49600 x,y,z range (A): 50.74400 55.36500 57.84900 scale (grids/A): 2.769279 object centre (A): 14.94200 61.08050 16.57150 number of atom coordinates read : 2578 total number of charged atoms : 2442 net assigned charge : -0.9859928 assigned positive charge : 383.8508 centred at (gu) : 92.90879 82.16530 90.33732 assigned negative charge : -384.8379 centred at (gu) : 92.68496 82.77982 90.37862 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 162479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 78433 mr = 111364 m= 29086 mr = 61453 m= 6998 mr = 22517 m= 885 mr = 4894 m= 30 mr = 504 m= 0 mr = 11 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 1.230000 number of dielectric boundary points 77168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19532 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.846186 object centre at (A) : 14.94200 61.08050 16.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0192020E-02 -0.3848774 midg,1,midg; midg,igrid,midg 0.8692357 -0.2464597 1,midg,midg; igrid,midg,midg 2.7660111E-02 -0.1005085 gauss-seidel spectral radius is 0.9992501 estimated iterations to convergence 288 setup time was (sec) 1.510000 now iterating at: 20:17:13 rms-change max change #iterations 9.679506 349.0085 at 10iterations 5.721898 139.3411 at 20iterations 3.339200 77.20844 at 30iterations 1.943264 42.23911 at 40iterations 1.125217 23.95855 at 50iterations 0.6491358 13.25275 at 60iterations 0.3748201 8.633683 at 70iterations 0.2159531 4.469466 at 80iterations 0.1237905 2.428035 at 90iterations 7.1212105E-02 1.534336 at 100iterations 4.0830340E-02 0.8272133 at 110iterations 2.3462579E-02 0.4269009 at 120iterations 1.3466205E-02 0.2738934 at 130iterations 7.7150585E-03 0.1419153 at 140iterations 4.4293203E-03 8.6959839E-02 at 150iterations 2.5492420E-03 5.0063133E-02 at 160iterations 1.4761888E-03 3.1202555E-02 at 170iterations 8.5646682E-04 1.6792297E-02 at 180iterations finished qdiffx linear iterations at : 20:17:22 total time elapsed so far: 10.91000 # loops : 180 mean,max change (kT/e) : 8.5646682E-04 1.6792297E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 20:17:23 11.077u 0.188s 0:11.85 94.9% 0+0k 0+0io 0pf+0w