Mon Oct 10 17:02:46 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 17:02:46 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 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: 0.5626679 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): -32.37400 30.89600 ymin,ymax (A): -20.68400 25.28200 zmin,zma (A): -7.689000 40.91600 x,y,z range (A): 63.27000 45.96600 48.60500 scale (grids/A): 0.5626679 object centre (A): -0.7390003 2.299000 16.61350 number of atom coordinates read : 2756 total number of charged atoms : 2614 net assigned charge : -1.499974 assigned positive charge : 410.7324 centred at (gu) : 90.72887 90.06239 89.46687 assigned negative charge : -412.2333 centred at (gu) : 90.75950 89.91335 89.37829 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5819 nv = 96 ne = 84 npr = 54957 no. pairs analyzed = 54957 no. exposed pairs = 3553 no. arc points = 25371 no. surface atoms = 1200 nbur = 1556 mkacc time = 0.1500000 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= 234 mr = 3019 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3413007E-09 7.2128936E-10 midg,1,midg; midg,igrid,midg -1.8518244E-09 1.5086314E-09 1,midg,midg; igrid,midg,midg 1.4767738E-10 -6.1283956E-10 gauss-seidel spectral radius is 0.9836913 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 17:02:47 rms-change max change #iterations 8.1442811E-02 13.83312 at 10iterations 5.8332207E-03 0.8806381 at 20iterations 4.1286895E-04 9.6218109E-02 at 30iterations 3.0237356E-05 4.2910278E-03 at 40iterations 2.1762924E-06 3.3283234E-04 at 50iterations finished qdiffx linear iterations at : 17:02:50 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 2.1762924E-06 3.3283234E-04 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 17:02:51 4.155u 0.257s 0:05.37 81.9% 0+0k 0+0io 4pf+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 17:02:52 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 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: 1.688004 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): -32.37400 30.89600 ymin,ymax (A): -20.68400 25.28200 zmin,zma (A): -7.689000 40.91600 x,y,z range (A): 63.27000 45.96600 48.60500 scale (grids/A): 1.688004 object centre (A): -0.7390003 2.299000 16.61350 number of atom coordinates read : 2756 total number of charged atoms : 2614 net assigned charge : -1.499974 assigned positive charge : 410.7324 centred at (gu) : 92.18557 90.18629 88.39989 assigned negative charge : -412.2333 centred at (gu) : 92.27811 89.73951 88.13461 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25371 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19573 mr = 43156 m= 2015 mr = 13506 m= 54 mr = 937 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1108 time to turn everything in is 0.5700000 number of dielectric boundary points 28006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20136 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) : 0.5626679 object centre at (A) : -0.7390003 2.299000 16.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7366071E-03 3.1618103E-03 midg,1,midg; midg,igrid,midg -1.6992347E-02 1.0147712E-02 1,midg,midg; igrid,midg,midg 6.5962113E-03 -4.1825950E-04 gauss-seidel spectral radius is 0.9982845 estimated iterations to convergence 192 setup time was (sec) 0.8700000 now iterating at: 17:02:53 rms-change max change #iterations 3.398413 182.3439 at 10iterations 1.445215 52.95450 at 20iterations 0.6163878 21.76777 at 30iterations 0.2632265 9.484790 at 40iterations 0.1123370 4.467533 at 50iterations 4.8057508E-02 1.746868 at 60iterations 2.0451000E-02 0.7524643 at 70iterations 8.7666567E-03 0.3276799 at 80iterations 3.7340862E-03 0.1283455 at 90iterations 1.5942081E-03 5.9104919E-02 at 100iterations 6.8098697E-04 2.2951126E-02 at 110iterations 2.9198392E-04 1.0313034E-02 at 120iterations finished qdiffx linear iterations at : 17:03:01 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 2.9198392E-04 1.0313034E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 17:03:02 9.360u 0.330s 0:10.36 93.5% 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 Mon Oct 10 2011 at 17:03:02 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 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: 2.532006 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): -32.37400 30.89600 ymin,ymax (A): -20.68400 25.28200 zmin,zma (A): -7.689000 40.91600 x,y,z range (A): 63.27000 45.96600 48.60500 scale (grids/A): 2.532006 object centre (A): -0.7390003 2.299000 16.61350 number of atom coordinates read : 2756 total number of charged atoms : 2614 net assigned charge : -1.499974 assigned positive charge : 410.7324 centred at (gu) : 93.27817 90.27933 87.59964 assigned negative charge : -412.2333 centred at (gu) : 93.41705 89.60944 87.20182 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25371 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68185 mr = 105487 m= 19475 mr = 54029 m= 2961 mr = 14536 m= 216 mr = 1873 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 3843 time to turn everything in is 1.400000 number of dielectric boundary points 63246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 20896 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) : 1.688004 object centre at (A) : -0.7390003 2.299000 16.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7477115E-02 4.0364139E-02 midg,1,midg; midg,igrid,midg -0.2072697 0.1578563 1,midg,midg; igrid,midg,midg 0.2418933 5.9652567E-02 gauss-seidel spectral radius is 0.9991641 estimated iterations to convergence 273 setup time was (sec) 1.720000 now iterating at: 17:03:04 rms-change max change #iterations 8.617223 268.2877 at 10iterations 4.834313 124.9330 at 20iterations 2.695067 60.78561 at 30iterations 1.509225 32.70767 at 40iterations 0.8405888 18.51756 at 50iterations 0.4680082 9.580535 at 60iterations 0.2599639 5.727554 at 70iterations 0.1444237 2.899378 at 80iterations 7.9954833E-02 1.773588 at 90iterations 4.4273432E-02 0.8937793 at 100iterations 2.4595985E-02 0.5462189 at 110iterations 1.3619727E-02 0.3183365 at 120iterations 7.5330199E-03 0.1608295 at 130iterations 4.1779056E-03 9.0641022E-02 at 140iterations 2.3126148E-03 4.8718452E-02 at 150iterations 1.2789407E-03 2.6294708E-02 at 160iterations 7.0913980E-04 1.4660597E-02 at 170iterations 3.9249574E-04 8.0051422E-03 at 180iterations finished qdiffx linear iterations at : 17:03:18 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 3.9249574E-04 8.0051422E-03 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.43000 DelPhi exited at 17:03:19 15.429u 0.319s 0:16.61 94.7% 0+0k 0+0io 0pf+0w