Tue Oct 11 06:23:53 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+sph.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 = amb.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 Tue Oct 11 2011 at 06:23:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1319 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8068537 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): -14.79500 25.78200 ymin,ymax (A): 41.68600 77.44400 zmin,zma (A): -4.691000 39.43100 x,y,z range (A): 40.57700 35.75800 44.12200 scale (grids/A): 0.8068537 object centre (A): 5.493500 59.56500 17.37000 number of atom coordinates read : 1319 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 89.95220 90.49210 89.84832 assigned negative charge : -198.9373 centred at (gu) : 90.09137 90.55939 89.55959 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 24542 no. pairs analyzed = 24542 no. exposed pairs = 1679 no. arc points = 12129 no. surface atoms = 584 nbur = 735 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 570 mr = 3716 m= 8 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 3175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 853 ## 64 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 6052 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9730926E-07 7.7025243E-07 midg,1,midg; midg,igrid,midg 2.9192572E-07 2.1498035E-08 1,midg,midg; igrid,midg,midg 4.7725348E-07 -1.3957347E-07 gauss-seidel spectral radius is 0.9919090 estimated iterations to convergence 90 setup time was (sec) 0.3000000 now iterating at: 06:23:54 rms-change max change #iterations 0.2714798 40.77637 at 10iterations 4.2233832E-02 5.740672 at 20iterations 6.7670164E-03 0.9967709 at 30iterations 1.1175191E-03 0.1529636 at 40iterations 2.2039488E-04 3.1570435E-02 at 50iterations finished qdiffx linear iterations at : 06:23:57 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2039488E-04 3.1570435E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:23:57 3.291u 0.183s 0:04.16 83.4% 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 Tue Oct 11 2011 at 06:23:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1319 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.420561 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): -14.79500 25.78200 ymin,ymax (A): 41.68600 77.44400 zmin,zma (A): -4.691000 39.43100 x,y,z range (A): 40.57700 35.75800 44.12200 scale (grids/A): 2.420561 object centre (A): 5.493500 59.56500 17.37000 number of atom coordinates read : 1319 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 89.85702 91.47660 89.54526 assigned negative charge : -198.9373 centred at (gu) : 90.27416 91.67848 88.67894 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12129 grid for indexing accessible points = 1.400000 m= 29666 mr = 46784 m= 7756 mr = 23214 m= 947 mr = 5649 m= 47 mr = 503 m= 0 mr = 15 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10122 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) : 0.8068537 object centre at (A) : 5.493500 59.56500 17.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7030960E-02 7.6370612E-02 midg,1,midg; midg,igrid,midg 2.6957588E-02 2.7624371E-03 1,midg,midg; igrid,midg,midg 7.6174825E-02 1.5226339E-02 gauss-seidel spectral radius is 0.9990003 estimated iterations to convergence 250 setup time was (sec) 0.5700000 now iterating at: 06:23:58 rms-change max change #iterations 4.576030 211.0421 at 10iterations 2.397179 84.12194 at 20iterations 1.256825 42.35319 at 30iterations 0.6534470 21.62564 at 40iterations 0.3415860 10.68084 at 50iterations 0.1792700 6.009103 at 60iterations 9.3569912E-02 2.750275 at 70iterations 4.8966449E-02 1.494864 at 80iterations 2.5603205E-02 0.7856979 at 90iterations 1.3369079E-02 0.4347458 at 100iterations 7.0366408E-03 0.2239571 at 110iterations 3.7211592E-03 0.1068020 at 120iterations finished qdiffx linear iterations at : 06:24:05 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 3.7211592E-03 0.1068020 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 06:24:06 7.824u 0.220s 0:08.50 94.5% 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 Tue Oct 11 2011 at 06:24:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1319 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.630842 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): -14.79500 25.78200 ymin,ymax (A): 41.68600 77.44400 zmin,zma (A): -4.691000 39.43100 x,y,z range (A): 40.57700 35.75800 44.12200 scale (grids/A): 3.630842 object centre (A): 5.493500 59.56500 17.37000 number of atom coordinates read : 1319 total number of charged atoms : 1268 net assigned charge : 2.500002 assigned positive charge : 201.4374 centred at (gu) : 89.78561 92.21498 89.31803 assigned negative charge : -198.9373 centred at (gu) : 90.41127 92.51775 88.01842 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12129 grid for indexing accessible points = 1.400000 m= 87810 mr = 112456 m= 42113 mr = 74037 m= 15340 mr = 35526 m= 3920 mr = 12586 m= 636 mr = 2933 m= 69 mr = 414 m= 0 mr = 36 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 65574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 10144 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) : 2.420561 object centre at (A) : 5.493500 59.56500 17.37000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7380074 0.4705201 midg,1,midg; midg,igrid,midg 0.1602075 3.5152704E-02 1,midg,midg; igrid,midg,midg 0.5323354 5.4119926E-02 gauss-seidel spectral radius is 0.9993312 estimated iterations to convergence 305 setup time was (sec) 1.310000 now iterating at: 06:24:07 rms-change max change #iterations 9.680616 261.3415 at 10iterations 5.856724 133.6871 at 20iterations 3.521317 86.02686 at 30iterations 2.117294 45.36708 at 40iterations 1.262199 27.11442 at 50iterations 0.7543402 15.97326 at 60iterations 0.4489287 7.928363 at 70iterations 0.2676892 5.077497 at 80iterations 0.1594505 2.952758 at 90iterations 9.4548345E-02 1.674194 at 100iterations 5.6216810E-02 1.096451 at 110iterations 3.3328027E-02 0.5878305 at 120iterations 1.9791653E-02 0.3548684 at 130iterations 1.1736545E-02 0.2025394 at 140iterations 6.9696880E-03 0.1360855 at 150iterations 4.1628038E-03 8.0005646E-02 at 160iterations 2.5094736E-03 4.8942566E-02 at 170iterations 1.5382373E-03 2.7801514E-02 at 180iterations finished qdiffx linear iterations at : 06:24:19 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 1.5382373E-03 2.7801514E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 06:24:19 12.516u 0.215s 0:13.23 96.1% 0+0k 0+0io 0pf+0w