Tue Oct 11 06:54:19 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 Tue Oct 11 2011 at 06:54:19 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 = 2928 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5655911 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): -18.61400 44.32900 ymin,ymax (A): 21.70200 79.80500 zmin,zma (A): -70.69500 -21.83700 x,y,z range (A): 62.94300 58.10300 48.85800 scale (grids/A): 0.5655911 object centre (A): 12.85750 50.75350 -46.26600 number of atom coordinates read : 2928 total number of charged atoms : 2788 net assigned charge : -4.999984 assigned positive charge : 426.9405 centred at (gu) : 89.84101 90.13913 88.90442 assigned negative charge : -431.9411 centred at (gu) : 89.83709 90.34844 88.90292 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6193 nv = 96 ne = 84 npr = 60028 no. pairs analyzed = 60028 no. exposed pairs = 3695 no. arc points = 26085 no. surface atoms = 1253 nbur = 1675 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 260 mr = 3255 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2592 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7866 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5915108E-10 -4.8625626E-10 midg,1,midg; midg,igrid,midg 1.9587725E-09 -3.5764929E-09 1,midg,midg; igrid,midg,midg -7.2301592E-10 -5.7258592E-10 gauss-seidel spectral radius is 0.9838715 estimated iterations to convergence 65 setup time was (sec) 0.5600000 now iterating at: 06:54:20 rms-change max change #iterations 8.7756835E-02 13.76420 at 10iterations 6.5266597E-03 1.052399 at 20iterations 5.4108817E-04 0.1073532 at 30iterations 9.7630233E-05 2.1614075E-02 at 40iterations 3.1209693E-05 7.2116852E-03 at 50iterations finished qdiffx linear iterations at : 06:54:22 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.1209693E-05 7.2116852E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:54:23 3.367u 0.196s 0:03.88 91.4% 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 06:54:23 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 = 2928 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: 1.696773 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): -18.61400 44.32900 ymin,ymax (A): 21.70200 79.80500 zmin,zma (A): -70.69500 -21.83700 x,y,z range (A): 62.94300 58.10300 48.85800 scale (grids/A): 1.696773 object centre (A): 12.85750 50.75350 -46.26600 number of atom coordinates read : 2928 total number of charged atoms : 2788 net assigned charge : -4.999984 assigned positive charge : 426.9405 centred at (gu) : 89.52202 90.41644 86.71274 assigned negative charge : -431.9411 centred at (gu) : 89.51089 91.04478 86.70834 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 67432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26085 grid for indexing accessible points = 1.400000 m= 22633 mr = 45749 m= 2749 mr = 16306 m= 74 mr = 1470 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21562 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) : 0.5655911 object centre at (A) : 12.85750 50.75350 -46.26600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3032030E-03 9.5138531E-03 midg,1,midg; midg,igrid,midg 3.2296235E-04 -2.2554785E-02 1,midg,midg; igrid,midg,midg -1.2963110E-02 -2.2661693E-02 gauss-seidel spectral radius is 0.9983235 estimated iterations to convergence 194 setup time was (sec) 0.8300000 now iterating at: 06:54:24 rms-change max change #iterations 3.551954 163.4830 at 10iterations 1.529011 52.40435 at 20iterations 0.6587486 24.38274 at 30iterations 0.2829125 10.38768 at 40iterations 0.1223335 4.621646 at 50iterations 5.2853458E-02 2.334934 at 60iterations 2.2855917E-02 0.8383904 at 70iterations 9.8517733E-03 0.3310394 at 80iterations 4.2622238E-03 0.1445060 at 90iterations 1.8535843E-03 6.7600250E-02 at 100iterations 8.0844754E-04 2.8812408E-02 at 110iterations 3.6010487E-04 1.2502670E-02 at 120iterations finished qdiffx linear iterations at : 06:54:30 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 3.6010487E-04 1.2502670E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 06:54:31 7.446u 0.193s 0:08.14 93.7% 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 Tue Oct 11 2011 at 06:54:31 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 = 2928 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: 2.545160 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): -18.61400 44.32900 ymin,ymax (A): 21.70200 79.80500 zmin,zma (A): -70.69500 -21.83700 x,y,z range (A): 62.94300 58.10300 48.85800 scale (grids/A): 2.545160 object centre (A): 12.85750 50.75350 -46.26600 number of atom coordinates read : 2928 total number of charged atoms : 2788 net assigned charge : -4.999984 assigned positive charge : 426.9405 centred at (gu) : 89.28270 90.62440 85.06889 assigned negative charge : -431.9411 centred at (gu) : 89.26604 91.56699 85.06243 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 156389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26085 grid for indexing accessible points = 1.400000 m= 75303 mr = 111685 m= 24545 mr = 60437 m= 4429 mr = 19320 m= 280 mr = 3044 m= 10 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 66353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 22290 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) : 1.696773 object centre at (A) : 12.85750 50.75350 -46.26600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5778721E-02 0.1752400 midg,1,midg; midg,igrid,midg 2.1232992E-02 -0.1952610 1,midg,midg; igrid,midg,midg -0.2499447 -0.5549799 gauss-seidel spectral radius is 0.9991814 estimated iterations to convergence 276 setup time was (sec) 1.470000 now iterating at: 06:54:33 rms-change max change #iterations 8.916691 281.8576 at 10iterations 5.045069 108.0908 at 20iterations 2.849785 70.14108 at 30iterations 1.604065 32.85674 at 40iterations 0.9009255 18.94925 at 50iterations 0.5047376 10.98108 at 60iterations 0.2825505 5.627439 at 70iterations 0.1578519 3.296798 at 80iterations 8.8119864E-02 1.996784 at 90iterations 4.9212944E-02 1.008709 at 100iterations 2.7453607E-02 0.5355835 at 110iterations 1.5293087E-02 0.2927876 at 120iterations 8.5505927E-03 0.1668510 at 130iterations 4.7784592E-03 8.9930058E-02 at 140iterations 2.6712699E-03 5.3928375E-02 at 150iterations 1.4953222E-03 3.6022186E-02 at 160iterations 8.4398448E-04 1.7548561E-02 at 170iterations 4.8202917E-04 9.5138550E-03 at 180iterations finished qdiffx linear iterations at : 06:54:43 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 4.8202917E-04 9.5138550E-03 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 06:54:43 11.873u 0.271s 0:12.44 97.5% 0+0k 0+0io 0pf+0w