Sat Oct 15 11:25:43 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 Sat Oct 15 2011 at 11:25:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5640498 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): -20.89300 32.72200 ymin,ymax (A): -19.06800 30.81100 zmin,zma (A): -14.30100 48.81400 x,y,z range (A): 53.61500 49.87900 63.11500 scale (grids/A): 0.5640498 object centre (A): 5.914500 5.871499 17.25650 number of atom coordinates read : 3327 total number of charged atoms : 3191 net assigned charge : 3.000010 assigned positive charge : 512.2385 centred at (gu) : 90.25644 89.29607 90.88512 assigned negative charge : -509.2404 centred at (gu) : 90.42725 89.24718 90.79999 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6758 nv = 96 ne = 84 npr = 68674 no. pairs analyzed = 68674 no. exposed pairs = 3781 no. arc points = 25867 no. surface atoms = 1290 nbur = 2037 mkacc time = 0.1200000 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= 281 mr = 3797 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2748 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8873 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1021355E-10 1.9918793E-09 midg,1,midg; midg,igrid,midg -4.1470141E-10 9.1636243E-10 1,midg,midg; igrid,midg,midg 2.6512219E-09 -2.3207847E-09 gauss-seidel spectral radius is 0.9838029 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 11:25:43 rms-change max change #iterations 9.0814568E-02 15.94861 at 10iterations 6.8305121E-03 0.9791527 at 20iterations 5.7742436E-04 8.6465836E-02 at 30iterations 6.0181512E-05 8.5687637E-03 at 40iterations 8.8577690E-06 1.4200211E-03 at 50iterations finished qdiffx linear iterations at : 11:25:46 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 8.8577690E-06 1.4200211E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 11:25:47 3.405u 0.169s 0:04.13 86.1% 0+0k 0+0io 6pf+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 Sat Oct 15 2011 at 11:25:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.692149 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): -20.89300 32.72200 ymin,ymax (A): -19.06800 30.81100 zmin,zma (A): -14.30100 48.81400 x,y,z range (A): 53.61500 49.87900 63.11500 scale (grids/A): 1.692149 object centre (A): 5.914500 5.871499 17.25650 number of atom coordinates read : 3327 total number of charged atoms : 3191 net assigned charge : 3.000010 assigned positive charge : 512.2385 centred at (gu) : 90.76836 87.88725 92.65456 assigned negative charge : -509.2404 centred at (gu) : 91.28165 87.74146 92.39977 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 75669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25867 grid for indexing accessible points = 1.400000 m= 24398 mr = 54216 m= 2798 mr = 17672 m= 104 mr = 1567 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3700000 number of dielectric boundary points 29489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 311 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 24649 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) : 0.5640498 object centre at (A) : 5.914500 5.871499 17.25650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4829105E-02 1.8610442E-02 midg,1,midg; midg,igrid,midg -9.6561788E-03 3.1088369E-03 1,midg,midg; igrid,midg,midg 2.5815185E-02 -1.0202649E-02 gauss-seidel spectral radius is 0.9983396 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 11:25:48 rms-change max change #iterations 3.845954 180.8406 at 10iterations 1.656593 69.48346 at 20iterations 0.7182834 24.29262 at 30iterations 0.3128364 10.25055 at 40iterations 0.1364816 4.937598 at 50iterations 5.9263341E-02 1.876850 at 60iterations 2.5668537E-02 0.8718300 at 70iterations 1.1124517E-02 0.4321270 at 80iterations 4.8448285E-03 0.1744184 at 90iterations 2.1097998E-03 7.2147369E-02 at 100iterations 9.1534172E-04 3.2257557E-02 at 110iterations 3.9918191E-04 1.2784958E-02 at 120iterations finished qdiffx linear iterations at : 11:25:55 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 3.9918191E-04 1.2784958E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 11:25:56 7.853u 0.210s 0:09.59 84.0% 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 Sat Oct 15 2011 at 11:25:56 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.538224 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): -20.89300 32.72200 ymin,ymax (A): -19.06800 30.81100 zmin,zma (A): -14.30100 48.81400 x,y,z range (A): 53.61500 49.87900 63.11500 scale (grids/A): 2.538224 object centre (A): 5.914500 5.871499 17.25650 number of atom coordinates read : 3327 total number of charged atoms : 3191 net assigned charge : 3.000010 assigned positive charge : 512.2385 centred at (gu) : 91.15254 86.83051 93.98164 assigned negative charge : -509.2404 centred at (gu) : 91.92229 86.61214 93.59959 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 176067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25867 grid for indexing accessible points = 1.400000 m= 84018 mr = 131879 m= 25523 mr = 68884 m= 4573 mr = 19987 m= 426 mr = 3168 m= 16 mr = 243 m= 0 mr = 6 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.9000000 number of dielectric boundary points 66456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 25504 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) : 1.692149 object centre at (A) : 5.914500 5.871499 17.25650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4756489 0.3617008 midg,1,midg; midg,igrid,midg -0.1590359 6.5788023E-02 1,midg,midg; igrid,midg,midg 0.4316435 -0.1646551 gauss-seidel spectral radius is 0.9991843 estimated iterations to convergence 276 setup time was (sec) 1.130000 now iterating at: 11:26:00 rms-change max change #iterations 9.570810 290.6420 at 10iterations 5.380543 116.0541 at 20iterations 3.030996 63.31367 at 30iterations 1.698037 31.93613 at 40iterations 0.9527374 18.34431 at 50iterations 0.5340390 10.48817 at 60iterations 0.2986976 5.618043 at 70iterations 0.1667958 2.984297 at 80iterations 9.3195640E-02 1.780622 at 90iterations 5.2179195E-02 1.045285 at 100iterations 2.9118691E-02 0.6006470 at 110iterations 1.6265405E-02 0.3052759 at 120iterations 9.0895584E-03 0.1747704 at 130iterations 5.0814324E-03 9.6561432E-02 at 140iterations 2.8416093E-03 5.4870605E-02 at 150iterations 1.5903753E-03 3.0642986E-02 at 160iterations 8.8866014E-04 1.6323090E-02 at 170iterations 4.9792090E-04 9.3650818E-03 at 180iterations finished qdiffx linear iterations at : 11:26:11 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 4.9792090E-04 9.3650818E-03 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 11:26:12 12.868u 0.236s 0:15.79 82.9% 0+0k 0+0io 0pf+0w