Sun Oct 9 20:00:45 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 20:00:45 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5309 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 0.5471451 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): 3.171000 67.61200 ymin,ymax (A): -8.822000 52.95100 zmin,zma (A): -2.171000 62.89400 x,y,z range (A): 64.44100 61.77300 65.06500 scale (grids/A): 0.5471451 object centre (A): 35.39150 22.06450 30.36150 number of atom coordinates read : 5309 total number of charged atoms : 5167 net assigned charge : 2.544052 assigned positive charge : 821.2935 centred at (gu) : 88.10407 89.26688 89.33535 assigned negative charge : -818.7556 centred at (gu) : 88.00397 89.28054 89.30527 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 10118 nv = 96 ne = 84 npr = 109067 no. pairs analyzed = 109067 no. exposed pairs = 5955 no. arc points = 40823 no. surface atoms = 2033 nbur = 3276 mkacc time = 0.1900000 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= 403 mr = 5819 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4164 ## 483 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 13526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2598022E-10 4.8757332E-10 midg,1,midg; midg,igrid,midg 4.3994422E-10 1.7822948E-11 1,midg,midg; igrid,midg,midg -1.7788279E-09 9.0771779E-10 gauss-seidel spectral radius is 0.9829397 estimated iterations to convergence 63 setup time was (sec) 0.5200000 now iterating at: 20:00:46 rms-change max change #iterations 0.1069124 13.02900 at 10iterations 1.0766125E-02 1.541161 at 20iterations 3.6517910E-03 0.5365105 at 30iterations 1.6427749E-03 0.2372284 at 40iterations 7.5272983E-04 0.1049194 at 50iterations finished qdiffx linear iterations at : 20:00:49 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.5272983E-04 0.1049194 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 20:00:49 3.480u 0.184s 0:03.94 92.8% 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 20:00:49 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5309 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 1.641435 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): 3.171000 67.61200 ymin,ymax (A): -8.822000 52.95100 zmin,zma (A): -2.171000 62.89400 x,y,z range (A): 64.44100 61.77300 65.06500 scale (grids/A): 1.641435 object centre (A): 35.39150 22.06450 30.36150 number of atom coordinates read : 5309 total number of charged atoms : 5167 net assigned charge : 2.544052 assigned positive charge : 821.2935 centred at (gu) : 84.31081 87.79923 88.00446 assigned negative charge : -818.7556 centred at (gu) : 84.01199 87.84181 87.91589 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 114805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 37325 mr = 83850 m= 4139 mr = 26728 m= 132 mr = 2086 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 681 time to turn everything in is 0.5200000 number of dielectric boundary points 43727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 440 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 39601 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) : 0.5471451 object centre at (A) : 35.39150 22.06450 30.36150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0985132E-02 -6.1319992E-03 midg,1,midg; midg,igrid,midg 1.8292056E-02 1.0271467E-02 1,midg,midg; igrid,midg,midg -1.8353559E-02 4.2085601E-03 gauss-seidel spectral radius is 0.9984063 estimated iterations to convergence 199 setup time was (sec) 0.7400000 now iterating at: 20:00:50 rms-change max change #iterations 4.835612 181.8409 at 10iterations 2.135266 61.30293 at 20iterations 0.9415083 25.31577 at 30iterations 0.4171628 11.94815 at 40iterations 0.1859197 5.586063 at 50iterations 8.2627982E-02 2.197044 at 60iterations 3.7547305E-02 1.047852 at 70iterations 1.7726578E-02 0.5131320 at 80iterations 9.0513807E-03 0.2816086 at 90iterations 5.2581718E-03 0.1790237 at 100iterations 3.4351763E-03 0.1095772 at 110iterations 2.4162575E-03 7.2860718E-02 at 120iterations finished qdiffx linear iterations at : 20:00:57 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.4162575E-03 7.2860718E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 20:00:58 7.941u 0.206s 0:08.64 94.2% 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 20:00:58 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5309 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 2.462153 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): 3.171000 67.61200 ymin,ymax (A): -8.822000 52.95100 zmin,zma (A): -2.171000 62.89400 x,y,z range (A): 64.44100 61.77300 65.06500 scale (grids/A): 2.462153 object centre (A): 35.39150 22.06450 30.36150 number of atom coordinates read : 5309 total number of charged atoms : 5167 net assigned charge : 2.544052 assigned positive charge : 821.2935 centred at (gu) : 81.46581 86.69853 87.00636 assigned negative charge : -818.7556 centred at (gu) : 81.01805 86.76274 86.87369 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 267277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 129988 mr = 204148 m= 38376 mr = 105990 m= 6691 mr = 29372 m= 587 mr = 4423 m= 21 mr = 323 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 2176 time to turn everything in is 1.350000 number of dielectric boundary points 98684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 41289 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) : 1.641435 object centre at (A) : 35.39150 22.06450 30.36150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3510638 -0.2009765 midg,1,midg; midg,igrid,midg 0.1819387 4.2825527E-02 1,midg,midg; igrid,midg,midg -0.4331305 9.5448248E-02 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.590000 now iterating at: 20:01:00 rms-change max change #iterations 12.26855 321.4322 at 10iterations 7.199704 141.4561 at 20iterations 4.191115 81.22347 at 30iterations 2.433145 43.65955 at 40iterations 1.408111 24.25213 at 50iterations 0.8128932 14.52720 at 60iterations 0.4687508 8.927504 at 70iterations 0.2697928 4.842577 at 80iterations 0.1552773 2.336239 at 90iterations 8.9622661E-02 1.426575 at 100iterations 5.1826384E-02 0.8451996 at 110iterations 3.0248510E-02 0.5255249 at 120iterations 1.7950345E-02 0.3358498 at 130iterations 1.0909407E-02 0.2051773 at 140iterations 6.9744783E-03 0.1353413 at 150iterations 4.7375453E-03 9.7209930E-02 at 160iterations 3.4405873E-03 6.5704346E-02 at 170iterations 2.6339684E-03 5.0449371E-02 at 180iterations finished qdiffx linear iterations at : 20:01:11 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 2.6339684E-03 5.0449371E-02 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 20:01:12 13.443u 0.198s 0:13.92 97.9% 0+0k 0+0io 0pf+0w