Sun Oct 9 18:12:04 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 Sun Oct 9 2011 at 18:12:04 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5468258 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): 3.202000 68.30500 ymin,ymax (A): -9.213000 53.47600 zmin,zma (A): -2.660000 61.64500 x,y,z range (A): 65.10300 62.68900 64.30499 scale (grids/A): 0.5468258 object centre (A): 35.75350 22.13150 29.49250 number of atom coordinates read : 5001 total number of charged atoms : 4857 net assigned charge : -0.8649487 assigned positive charge : 770.7579 centred at (gu) : 87.55739 89.38882 89.55483 assigned negative charge : -771.6286 centred at (gu) : 87.43668 89.41086 89.55885 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9842 nv = 96 ne = 84 npr = 100516 no. pairs analyzed = 100516 no. exposed pairs = 5949 no. arc points = 40420 no. surface atoms = 2031 nbur = 2970 mkacc time = 0.2200000 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 = 1.568000 m= 436 mr = 5556 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4109 ## 472 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 12864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3648462E-11 -5.8288346E-11 midg,1,midg; midg,igrid,midg 2.8260871E-10 -2.3911850E-10 1,midg,midg; igrid,midg,midg -2.7285711E-09 7.5578022E-10 gauss-seidel spectral radius is 0.9829050 estimated iterations to convergence 63 setup time was (sec) 0.6700000 now iterating at: 18:12:05 rms-change max change #iterations 0.1013436 13.41127 at 10iterations 9.2138601E-03 1.422302 at 20iterations 2.7083999E-03 0.3176117 at 30iterations 1.2307082E-03 0.1397943 at 40iterations 5.8312027E-04 7.2184563E-02 at 50iterations finished qdiffx linear iterations at : 18:12:07 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 5.8312027E-04 7.2184563E-02 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 18:12:08 3.264u 0.152s 0:03.72 91.6% 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 Sun Oct 9 2011 at 18:12:08 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.640477 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): 3.202000 68.30500 ymin,ymax (A): -9.213000 53.47600 zmin,zma (A): -2.660000 61.64500 x,y,z range (A): 65.10300 62.68900 64.30499 scale (grids/A): 1.640477 object centre (A): 35.75350 22.13150 29.49250 number of atom coordinates read : 5001 total number of charged atoms : 4857 net assigned charge : -0.8649487 assigned positive charge : 770.7579 centred at (gu) : 82.67053 88.16528 88.66315 assigned negative charge : -771.6286 centred at (gu) : 82.31004 88.23244 88.67650 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 109770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 37907 mr = 79272 m= 4392 mr = 27228 m= 150 mr = 2280 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 43423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 412 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 37283 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) : 0.5468258 object centre at (A) : 35.75350 22.13150 29.49250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6848609E-02 -2.6368896E-02 midg,1,midg; midg,igrid,midg 1.6966680E-02 7.0925071E-03 1,midg,midg; igrid,midg,midg -2.6193226E-02 1.9998973E-02 gauss-seidel spectral radius is 0.9983900 estimated iterations to convergence 198 setup time was (sec) 0.9900000 now iterating at: 18:12:09 rms-change max change #iterations 4.708165 168.6142 at 10iterations 2.067178 72.41330 at 20iterations 0.9073408 24.98043 at 30iterations 0.3996057 12.95055 at 40iterations 0.1765672 5.460782 at 50iterations 7.7647984E-02 2.136309 at 60iterations 3.4737252E-02 0.9695692 at 70iterations 1.5835758E-02 0.5135651 at 80iterations 7.6997471E-03 0.2524338 at 90iterations 4.2005908E-03 0.1159058 at 100iterations 2.6439761E-03 7.3878288E-02 at 110iterations 1.8572608E-03 4.6449661E-02 at 120iterations finished qdiffx linear iterations at : 18:12:15 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 1.8572608E-03 4.6449661E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 18:12:15 7.136u 0.168s 0:07.60 95.9% 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 Sun Oct 9 2011 at 18:12:15 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.460716 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): 3.202000 68.30500 ymin,ymax (A): -9.213000 53.47600 zmin,zma (A): -2.660000 61.64500 x,y,z range (A): 65.10300 62.68900 64.30499 scale (grids/A): 2.460716 object centre (A): 35.75350 22.13150 29.49250 number of atom coordinates read : 5001 total number of charged atoms : 4857 net assigned charge : -0.8649487 assigned positive charge : 770.7579 centred at (gu) : 79.00547 87.24728 87.99442 assigned negative charge : -771.6286 centred at (gu) : 78.46503 87.34872 88.01479 start vw surface at 0.2000000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 255162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 128408 mr = 193201 m= 40012 mr = 104210 m= 6971 mr = 30764 m= 534 mr = 4670 m= 8 mr = 266 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 97984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 38825 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) : 1.640477 object centre at (A) : 35.75350 22.13150 29.49250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3149181 -0.5563388 midg,1,midg; midg,igrid,midg 0.1168061 -6.0292978E-02 1,midg,midg; igrid,midg,midg -0.5149492 0.3197782 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 2.110000 now iterating at: 18:12:18 rms-change max change #iterations 12.03211 312.7236 at 10iterations 7.079618 145.2571 at 20iterations 4.143143 89.91585 at 30iterations 2.410319 42.70637 at 40iterations 1.395058 26.70961 at 50iterations 0.8061679 14.67702 at 60iterations 0.4646835 9.124462 at 70iterations 0.2672272 4.555189 at 80iterations 0.1535573 2.585082 at 90iterations 8.8273644E-02 1.584848 at 100iterations 5.0907150E-02 0.8609009 at 110iterations 2.9470367E-02 0.5311136 at 120iterations 1.7357772E-02 0.3342190 at 130iterations 1.0467701E-02 0.1979446 at 140iterations 6.6174804E-03 0.1226918 at 150iterations 4.4772490E-03 8.3892822E-02 at 160iterations 3.2593657E-03 5.8207989E-02 at 170iterations 2.5266123E-03 4.4317245E-02 at 180iterations finished qdiffx linear iterations at : 18:12:28 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 2.5266123E-03 4.4317245E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 18:12:28 12.109u 0.169s 0:12.57 97.5% 0+0k 0+0io 0pf+0w