Mon Oct 10 10:21:01 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 Mon Oct 10 2011 at 10:21:01 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 = 2881 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: 0.5614699 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): 17.72000 74.75200 ymin,ymax (A): -46.10600 5.491000 zmin,zma (A): 7.979000 71.38400 x,y,z range (A): 57.03200 51.59700 63.40500 scale (grids/A): 0.5614699 object centre (A): 46.23600 -20.30750 39.68150 number of atom coordinates read : 2881 total number of charged atoms : 2731 net assigned charge : 9.000024 assigned positive charge : 420.6819 centred at (gu) : 92.26201 89.89676 89.10191 assigned negative charge : -411.6823 centred at (gu) : 92.51556 89.98032 89.08125 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6172 nv = 96 ne = 84 npr = 55087 no. pairs analyzed = 55087 no. exposed pairs = 4318 no. arc points = 31118 no. surface atoms = 1436 nbur = 1445 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 = 1.540000 m= 279 mr = 2729 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3132 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7869 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0558462E-09 1.0519604E-09 midg,1,midg; midg,igrid,midg 2.0138666E-09 1.7078730E-10 1,midg,midg; igrid,midg,midg 2.1632540E-09 -3.0808349E-09 gauss-seidel spectral radius is 0.9836491 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 10:21:02 rms-change max change #iterations 7.7696860E-02 15.85121 at 10iterations 5.5656596E-03 0.8773165 at 20iterations 3.9487213E-04 6.4300537E-02 at 30iterations 3.0167939E-05 5.0964355E-03 at 40iterations 2.6433829E-06 3.5858154E-04 at 50iterations finished qdiffx linear iterations at : 10:21:04 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.6433829E-06 3.5858154E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 10:21:05 3.563u 0.184s 0:04.03 92.8% 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 10:21:05 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 = 2881 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: 1.684410 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): 17.72000 74.75200 ymin,ymax (A): -46.10600 5.491000 zmin,zma (A): 7.979000 71.38400 x,y,z range (A): 57.03200 51.59700 63.40500 scale (grids/A): 1.684410 object centre (A): 46.23600 -20.30750 39.68150 number of atom coordinates read : 2881 total number of charged atoms : 2731 net assigned charge : 9.000024 assigned positive charge : 420.6819 centred at (gu) : 96.78549 89.68966 87.30535 assigned negative charge : -411.6823 centred at (gu) : 97.54647 89.94079 87.24350 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 67087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31118 grid for indexing accessible points = 1.400000 m= 19873 mr = 41415 m= 2209 mr = 12417 m= 68 mr = 955 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 340 time to turn everything in is 0.5400000 number of dielectric boundary points 34445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21082 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) : 0.5614699 object centre at (A) : 46.23600 -20.30750 39.68150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8267866E-02 1.4326537E-02 midg,1,midg; midg,igrid,midg 1.0867447E-02 1.1533097E-02 1,midg,midg; igrid,midg,midg 2.6299130E-02 9.6149248E-04 gauss-seidel spectral radius is 0.9983127 estimated iterations to convergence 193 setup time was (sec) 0.8400000 now iterating at: 10:21:06 rms-change max change #iterations 3.412989 183.0070 at 10iterations 1.455369 63.97630 at 20iterations 0.6233952 21.29939 at 30iterations 0.2666007 9.398281 at 40iterations 0.1141648 3.998150 at 50iterations 4.8783742E-02 1.855413 at 60iterations 2.0944223E-02 0.8841743 at 70iterations 8.9972559E-03 0.3230534 at 80iterations 3.8514796E-03 0.1381812 at 90iterations 1.6552170E-03 6.2810898E-02 at 100iterations 7.1202993E-04 2.4595737E-02 at 110iterations 3.0396500E-04 1.0424614E-02 at 120iterations finished qdiffx linear iterations at : 10:21:14 total time elapsed so far: 8.970000 # loops : 120 mean,max change (kT/e) : 3.0396500E-04 1.0424614E-02 energy calculations done at 8.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.170000 DelPhi exited at 10:21:15 9.169u 0.250s 0:09.76 96.4% 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 Mon Oct 10 2011 at 10:21:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2881 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: 2.526614 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): 17.72000 74.75200 ymin,ymax (A): -46.10600 5.491000 zmin,zma (A): 7.979000 71.38400 x,y,z range (A): 57.03200 51.59700 63.40500 scale (grids/A): 2.526614 object centre (A): 46.23600 -20.30750 39.68150 number of atom coordinates read : 2881 total number of charged atoms : 2731 net assigned charge : 9.000024 assigned positive charge : 420.6819 centred at (gu) : 100.1782 89.53427 85.95782 assigned negative charge : -411.6823 centred at (gu) : 101.3195 89.91109 85.86531 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 155441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31118 grid for indexing accessible points = 1.400000 m= 67827 mr = 102433 m= 19590 mr = 50497 m= 3336 mr = 13684 m= 267 mr = 1931 m= 12 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1054 time to turn everything in is 1.250000 number of dielectric boundary points 77822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 21839 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) : 1.684410 object centre at (A) : 46.23600 -20.30750 39.68150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5315533 0.2866634 midg,1,midg; midg,igrid,midg 9.7485341E-02 0.1384414 1,midg,midg; igrid,midg,midg 0.4123569 3.2208435E-02 gauss-seidel spectral radius is 0.9991902 estimated iterations to convergence 277 setup time was (sec) 1.580000 now iterating at: 10:21:17 rms-change max change #iterations 8.831974 307.5641 at 10iterations 5.094182 146.4088 at 20iterations 2.918957 71.20940 at 30iterations 1.661844 43.22079 at 40iterations 0.9397686 24.95000 at 50iterations 0.5307932 11.93428 at 60iterations 0.2995902 6.037086 at 70iterations 0.1684113 3.661182 at 80iterations 9.4587266E-02 2.038693 at 90iterations 5.2999381E-02 1.113052 at 100iterations 2.9745940E-02 0.6179615 at 110iterations 1.6661938E-02 0.3711395 at 120iterations 9.3249092E-03 0.1946207 at 130iterations 5.2168644E-03 0.1068039 at 140iterations 2.9215037E-03 5.8256149E-02 at 150iterations 1.6341232E-03 3.2161713E-02 at 160iterations 9.1366755E-04 1.9162178E-02 at 170iterations 5.1135727E-04 1.1737823E-02 at 180iterations finished qdiffx linear iterations at : 10:21:28 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 5.1135727E-04 1.1737823E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 10:21:28 12.942u 0.252s 0:13.48 97.8% 0+0k 0+0io 0pf+0w