Mon Oct 10 13:53:25 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 13:53:26 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5096 !!! WARNING: PLP 3297 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.3558826 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): 12.79000 112.8230 ymin,ymax (A): -30.72600 51.54800 zmin,zma (A): -6.439000 76.11300 x,y,z range (A): 100.0330 82.27400 82.55200 scale (grids/A): 0.3558826 object centre (A): 62.80650 10.41100 34.83700 number of atom coordinates read : 5096 total number of charged atoms : 4884 net assigned charge : 2.121048 assigned positive charge : 771.9909 centred at (gu) : 83.78591 86.67029 85.67148 assigned negative charge : -769.8755 centred at (gu) : 83.74413 86.67813 85.71594 start vw surface at 0.2500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 3630 nv = 96 ne = 84 npr = 100958 no. pairs analyzed = 100958 no. exposed pairs = 6202 no. arc points = 43050 no. surface atoms = 2112 nbur = 2984 mkacc time = 0.2400000 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 = 2.352000 m= 69 mr = 1673 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 2026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 797 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 4988 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0010706E-14 -1.3927173E-15 midg,1,midg; midg,igrid,midg 1.0222047E-14 2.9071888E-17 1,midg,midg; igrid,midg,midg -7.0744917E-14 9.9035219E-16 gauss-seidel spectral radius is 0.9601007 estimated iterations to convergence 42 setup time was (sec) 0.7600000 now iterating at: 13:53:27 rms-change max change #iterations 1.4011716E-02 3.373154 at 10iterations 2.7132321E-03 0.8585129 at 20iterations 8.5677853E-04 0.2645264 at 30iterations 2.7293517E-04 8.1962585E-02 at 40iterations 8.7268068E-05 2.5577545E-02 at 50iterations finished qdiffx linear iterations at : 13:53:30 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 8.7268068E-05 2.5577545E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 13:53:32 3.909u 0.206s 0:05.80 70.6% 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 13:53:32 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5096 !!! WARNING: PLP 3297 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= 0.2100000 grid size : 179 scale,in grids/A, set to be: 1.067648 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): 12.79000 112.8230 ymin,ymax (A): -30.72600 51.54800 zmin,zma (A): -6.439000 76.11300 x,y,z range (A): 100.0330 82.27400 82.55200 scale (grids/A): 1.067648 object centre (A): 62.80650 10.41100 34.83700 number of atom coordinates read : 5096 total number of charged atoms : 4884 net assigned charge : 2.121048 assigned positive charge : 771.9909 centred at (gu) : 71.35625 80.00935 77.01346 assigned negative charge : -769.8755 centred at (gu) : 71.23229 80.03420 77.14732 start vw surface at 0.3300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 45087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43050 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.184000 m= 8227 mr = 29529 m= 180 mr = 4361 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 19596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1069 ## 82 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 30064 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) : 0.3558826 object centre at (A) : 62.80650 10.41100 34.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8031747E-04 -7.0762166E-05 midg,1,midg; midg,igrid,midg 9.7718509E-04 8.1822189E-05 1,midg,midg; igrid,midg,midg -6.4694614E-04 -2.3630746E-06 gauss-seidel spectral radius is 0.9956926 estimated iterations to convergence 122 setup time was (sec) 0.8500000 now iterating at: 13:53:33 rms-change max change #iterations 1.480147 114.0748 at 10iterations 0.3842257 21.33951 at 20iterations 0.1019994 6.366264 at 30iterations 2.8245155E-02 1.643097 at 40iterations 9.8597296E-03 0.6308517 at 50iterations 4.9324376E-03 0.2902985 at 60iterations 3.0601227E-03 0.1767159 at 70iterations 2.0058737E-03 0.1135330 at 80iterations 1.3245292E-03 7.3970795E-02 at 90iterations 8.7712670E-04 4.8442841E-02 at 100iterations 5.8076240E-04 3.1780243E-02 at 110iterations 3.8476288E-04 2.0866394E-02 at 120iterations finished qdiffx linear iterations at : 13:53:39 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 3.8476288E-04 2.0866394E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 13:53:40 7.312u 0.179s 0:08.08 92.5% 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 13:53:40 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5096 !!! WARNING: PLP 3297 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= 0.1900000 grid size : 179 scale,in grids/A, set to be: 1.601472 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): 12.79000 112.8230 ymin,ymax (A): -30.72600 51.54800 zmin,zma (A): -6.439000 76.11300 x,y,z range (A): 100.0330 82.27400 82.55200 scale (grids/A): 1.601472 object centre (A): 62.80650 10.41100 34.83700 number of atom coordinates read : 5096 total number of charged atoms : 4884 net assigned charge : 2.121048 assigned positive charge : 771.9909 centred at (gu) : 62.03382 75.01386 70.51966 assigned negative charge : -769.8755 centred at (gu) : 61.84840 75.05131 70.72100 start vw surface at 0.3000000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 106825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43050 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.156000 m= 35845 mr = 75018 m= 3836 mr = 25395 m= 93 mr = 1857 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 44327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 433 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 37148 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) : 1.067648 object centre at (A) : 62.80650 10.41100 34.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0707986E-02 -2.7776829E-03 midg,1,midg; midg,igrid,midg 5.0559744E-02 2.4482249E-03 1,midg,midg; igrid,midg,midg -8.8819705E-02 -2.1711992E-04 gauss-seidel spectral radius is 0.9981524 estimated iterations to convergence 185 setup time was (sec) 1.300000 now iterating at: 13:53:41 rms-change max change #iterations 5.111641 185.1943 at 10iterations 2.210054 78.46553 at 20iterations 0.9452673 33.62025 at 30iterations 0.4036516 14.77760 at 40iterations 0.1704225 5.143394 at 50iterations 7.2657883E-02 2.098823 at 60iterations 3.1438235E-02 0.9706078 at 70iterations 1.4208470E-02 0.4703636 at 80iterations 7.1341144E-03 0.2498169 at 90iterations 4.2148498E-03 0.1627197 at 100iterations 2.8620355E-03 9.8045349E-02 at 110iterations 2.0771404E-03 7.0690155E-02 at 120iterations 1.5477337E-03 5.1548004E-02 at 130iterations 1.1643183E-03 3.8063049E-02 at 140iterations 8.7845110E-04 2.8308868E-02 at 150iterations 6.6331623E-04 2.1141052E-02 at 160iterations 5.0122692E-04 1.5811920E-02 at 170iterations 3.7894622E-04 1.1837006E-02 at 180iterations finished qdiffx linear iterations at : 13:53:51 total time elapsed so far: 10.93000 # loops : 180 mean,max change (kT/e) : 3.7894622E-04 1.1837006E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 13:53:52 11.128u 0.156s 0:11.77 95.7% 0+0k 0+0io 0pf+0w