Sat Oct 15 13:19:29 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 13:19:34 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5108 !!! 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: 0.5573124 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): 3.221000 64.79800 ymin,ymax (A): -8.160000 54.50700 zmin,zma (A): -1.942000 61.93600 x,y,z range (A): 61.57700 62.66700 63.87800 scale (grids/A): 0.5573124 object centre (A): 34.00950 23.17350 29.99700 number of atom coordinates read : 5108 total number of charged atoms : 4959 net assigned charge : 2.621041 assigned positive charge : 786.5300 centred at (gu) : 88.13836 88.92213 89.20526 assigned negative charge : -783.9145 centred at (gu) : 88.01992 88.94852 89.22038 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10396 nv = 96 ne = 84 npr = 102435 no. pairs analyzed = 102435 no. exposed pairs = 6082 no. arc points = 41127 no. surface atoms = 2055 nbur = 3053 mkacc time = 0.2900000 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= 524 mr = 5909 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 4973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4202 ## 468 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 13521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7114808E-10 1.8438044E-11 midg,1,midg; midg,igrid,midg 9.7748065E-10 -1.3532293E-10 1,midg,midg; igrid,midg,midg -2.9277039E-09 1.4916978E-09 gauss-seidel spectral radius is 0.9835511 estimated iterations to convergence 64 setup time was (sec) 0.8500000 now iterating at: 13:19:38 rms-change max change #iterations 0.1132248 15.32863 at 10iterations 1.0406092E-02 1.595703 at 20iterations 3.5808019E-03 0.4187431 at 30iterations 1.9271942E-03 0.2350159 at 40iterations 1.0515694E-03 0.1295986 at 50iterations finished qdiffx linear iterations at : 13:19:48 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 1.0515694E-03 0.1295986 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 13:19:50 4.315u 0.269s 0:17.33 26.3% 0+0k 0+0io 3pf+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 13:19:55 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5108 !!! 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: 1.671937 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): 3.221000 64.79800 ymin,ymax (A): -8.160000 54.50700 zmin,zma (A): -1.942000 61.93600 x,y,z range (A): 61.57700 62.66700 63.87800 scale (grids/A): 1.671937 object centre (A): 34.00950 23.17350 29.99700 number of atom coordinates read : 5108 total number of charged atoms : 4959 net assigned charge : 2.621041 assigned positive charge : 786.5300 centred at (gu) : 84.41372 86.76483 87.61434 assigned negative charge : -783.9145 centred at (gu) : 84.05978 86.84551 87.66116 start vw surface at 0.2200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 114784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41127 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 41851 mr = 82636 m= 5494 mr = 30543 m= 182 mr = 2905 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 117 time to turn everything in is 1.010000 number of dielectric boundary points 46223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 411 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 38199 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) : 0.5573124 object centre at (A) : 34.00950 23.17350 29.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4000935E-02 -2.7732018E-02 midg,1,midg; midg,igrid,midg 1.2232052E-02 1.2318213E-02 1,midg,midg; igrid,midg,midg -1.8092897E-02 3.6671102E-02 gauss-seidel spectral radius is 0.9984662 estimated iterations to convergence 203 setup time was (sec) 1.320000 now iterating at: 13:20:01 rms-change max change #iterations 4.901625 192.1698 at 10iterations 2.189915 66.58055 at 20iterations 0.9806406 29.62564 at 30iterations 0.4390815 11.91629 at 40iterations 0.1977825 5.541893 at 50iterations 8.8834360E-02 2.429174 at 60iterations 4.0430311E-02 1.106747 at 70iterations 1.8802142E-02 0.5062733 at 80iterations 9.4005391E-03 0.2774849 at 90iterations 5.3414865E-03 0.1516914 at 100iterations 3.5436740E-03 0.1068268 at 110iterations 2.6246184E-03 6.5826416E-02 at 120iterations finished qdiffx linear iterations at : 13:20:26 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 2.6246184E-03 6.5826416E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 13:20:28 10.124u 0.290s 0:33.01 31.5% 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 Sat Oct 15 2011 at 13:20:30 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5108 !!! 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: 2.507906 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): 3.221000 64.79800 ymin,ymax (A): -8.160000 54.50700 zmin,zma (A): -1.942000 61.93600 x,y,z range (A): 61.57700 62.66700 63.87800 scale (grids/A): 2.507906 object centre (A): 34.00950 23.17350 29.99700 number of atom coordinates read : 5108 total number of charged atoms : 4959 net assigned charge : 2.621041 assigned positive charge : 786.5300 centred at (gu) : 81.62018 85.14697 86.42136 assigned negative charge : -783.9145 centred at (gu) : 81.08965 85.26836 86.49174 start vw surface at 0.2100000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 266190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41127 grid for indexing accessible points = 1.400000 m= 138044 mr = 200754 m= 47233 mr = 112820 m= 8940 mr = 36921 m= 764 mr = 6076 m= 15 mr = 358 m= 0 mr = 0 time to grow re-entrant surface = 1.640000 no. cavity mid-points inaccessible to solvent = 415 time to turn everything in is 2.580000 number of dielectric boundary points 104257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.750000 number of grid points assigned charge 39630 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) : 1.671937 object centre at (A) : 34.00950 23.17350 29.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4612091 -0.6904548 midg,1,midg; midg,igrid,midg -9.3997873E-02 0.1175903 1,midg,midg; igrid,midg,midg -0.4079816 0.5196450 gauss-seidel spectral radius is 0.9992642 estimated iterations to convergence 291 setup time was (sec) 2.930000 now iterating at: 13:20:42 rms-change max change #iterations 12.35526 310.2770 at 10iterations 7.299236 155.5851 at 20iterations 4.282845 92.36000 at 30iterations 2.504025 47.50043 at 40iterations 1.462025 27.29019 at 50iterations 0.8504506 14.96538 at 60iterations 0.4940445 7.971069 at 70iterations 0.2865605 4.598099 at 80iterations 0.1660239 2.487869 at 90iterations 9.6312843E-02 1.726503 at 100iterations 5.5851709E-02 0.9076157 at 110iterations 3.2419398E-02 0.5071869 at 120iterations 1.9009819E-02 0.3317032 at 130iterations 1.1347122E-02 0.2127228 at 140iterations 6.9714100E-03 0.1214733 at 150iterations 4.5421608E-03 7.6179504E-02 at 160iterations 3.2051830E-03 5.1910400E-02 at 170iterations 2.4399627E-03 3.9947510E-02 at 180iterations finished qdiffx linear iterations at : 13:21:26 total time elapsed so far: 17.53000 # loops : 180 mean,max change (kT/e) : 2.4399627E-03 3.9947510E-02 energy calculations done at 17.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 13:21:28 17.708u 0.299s 0:58.14 30.9% 0+0k 0+0io 0pf+0w