Sun Oct 9 19:59:33 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 19:59:33 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5603211 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): 32.38700 88.21600 ymin,ymax (A): -40.36100 15.61800 zmin,zma (A): 6.724000 70.25900 x,y,z range (A): 55.82900 55.97900 63.53500 scale (grids/A): 0.5603211 object centre (A): 60.30150 -12.37150 38.49150 number of atom coordinates read : 3825 total number of charged atoms : 3670 net assigned charge : 9.500013 assigned positive charge : 593.4813 centred at (gu) : 89.30920 89.95480 90.09048 assigned negative charge : -583.9839 centred at (gu) : 89.43938 89.96127 90.11208 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7965 nv = 96 ne = 84 npr = 74517 no. pairs analyzed = 74517 no. exposed pairs = 5119 no. arc points = 36269 no. surface atoms = 1689 nbur = 2136 mkacc time = 0.1600000 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= 356 mr = 4001 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3691 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10319 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2984984E-09 7.0467893E-10 midg,1,midg; midg,igrid,midg 1.1162166E-09 9.0443586E-10 1,midg,midg; igrid,midg,midg 3.4254117E-09 -7.8589452E-10 gauss-seidel spectral radius is 0.9836420 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 19:59:34 rms-change max change #iterations 9.4606526E-02 13.37497 at 10iterations 7.2476449E-03 1.073601 at 20iterations 1.2002008E-03 0.1770382 at 30iterations 4.3882604E-04 6.4636230E-02 at 40iterations 1.7968386E-04 2.5625229E-02 at 50iterations finished qdiffx linear iterations at : 19:59:36 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.7968386E-04 2.5625229E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 19:59:37 3.235u 0.133s 0:03.65 92.0% 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 Sun Oct 9 2011 at 19:59:37 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.680963 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): 32.38700 88.21600 ymin,ymax (A): -40.36100 15.61800 zmin,zma (A): 6.724000 70.25900 x,y,z range (A): 55.82900 55.97900 63.53500 scale (grids/A): 1.680963 object centre (A): 60.30150 -12.37150 38.49150 number of atom coordinates read : 3825 total number of charged atoms : 3670 net assigned charge : 9.500013 assigned positive charge : 593.4813 centred at (gu) : 87.92635 89.86355 90.27019 assigned negative charge : -583.9839 centred at (gu) : 88.31805 89.88363 90.33603 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36269 grid for indexing accessible points = 1.400000 m= 30180 mr = 58585 m= 3773 mr = 20646 m= 117 mr = 1909 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 39959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 28226 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) : 0.5603211 object centre at (A) : 60.30150 -12.37150 38.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8814119E-03 5.9728841E-03 midg,1,midg; midg,igrid,midg 2.9183071E-02 2.4979969E-02 1,midg,midg; igrid,midg,midg 9.4195884E-03 -1.3091314E-03 gauss-seidel spectral radius is 0.9983900 estimated iterations to convergence 198 setup time was (sec) 0.8500000 now iterating at: 19:59:38 rms-change max change #iterations 4.141295 163.8581 at 10iterations 1.815666 60.17516 at 20iterations 0.7955101 27.59004 at 30iterations 0.3487876 12.37024 at 40iterations 0.1533263 4.768691 at 50iterations 6.7119032E-02 2.046860 at 60iterations 2.9553469E-02 1.130447 at 70iterations 1.3065543E-02 0.4072647 at 80iterations 5.8693029E-03 0.1899261 at 90iterations 2.6902864E-03 8.5662365E-02 at 100iterations 1.3321554E-03 4.8326492E-02 at 110iterations 7.4110663E-04 2.3601532E-02 at 120iterations finished qdiffx linear iterations at : 19:59:44 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 7.4110663E-04 2.3601532E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 19:59:44 7.076u 0.165s 0:07.59 95.2% 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 19:59:44 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3825 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: 2.521445 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): 32.38700 88.21600 ymin,ymax (A): -40.36100 15.61800 zmin,zma (A): 6.724000 70.25900 x,y,z range (A): 55.82900 55.97900 63.53500 scale (grids/A): 2.521445 object centre (A): 60.30150 -12.37150 38.49150 number of atom coordinates read : 3825 total number of charged atoms : 3670 net assigned charge : 9.500013 assigned positive charge : 593.4813 centred at (gu) : 86.88921 89.79505 90.40495 assigned negative charge : -583.9839 centred at (gu) : 87.47709 89.82530 90.50395 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 201858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36269 grid for indexing accessible points = 1.400000 m= 99223 mr = 143685 m= 32888 mr = 77707 m= 6257 mr = 24737 m= 542 mr = 4097 m= 8 mr = 245 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 90305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 29349 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) : 1.680963 object centre at (A) : 60.30150 -12.37150 38.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1759905 3.3514973E-02 midg,1,midg; midg,igrid,midg 0.4075629 0.4008498 1,midg,midg; igrid,midg,midg 2.9041849E-02 3.3072375E-02 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.770000 now iterating at: 19:59:46 rms-change max change #iterations 10.72928 315.2953 at 10iterations 6.336406 150.5349 at 20iterations 3.700614 84.77719 at 30iterations 2.154153 46.62815 at 40iterations 1.245281 26.42961 at 50iterations 0.7190566 13.66757 at 60iterations 0.4147993 8.767743 at 70iterations 0.2378766 4.813632 at 80iterations 0.1360164 2.563236 at 90iterations 7.7862091E-02 1.784359 at 100iterations 4.4564828E-02 0.9464436 at 110iterations 2.5488073E-02 0.4554520 at 120iterations 1.4554269E-02 0.2879725 at 130iterations 8.3133131E-03 0.1691532 at 140iterations 4.7507412E-03 9.1602325E-02 at 150iterations 2.7312846E-03 5.6575775E-02 at 160iterations 1.5766812E-03 2.8787613E-02 at 170iterations 9.1800920E-04 1.8432617E-02 at 180iterations finished qdiffx linear iterations at : 19:59:56 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 9.1800920E-04 1.8432617E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 19:59:56 11.521u 0.143s 0:11.94 97.6% 0+0k 0+0io 0pf+0w