Mon Oct 10 13:54:03 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 Mon Oct 10 2011 at 13:54:03 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5096 !!! WARNING: HIQ 363 has a net charge of 0.5140 !!! 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= 0.1500000 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 : 2.135047 assigned positive charge : 775.2330 centred at (gu) : 83.78748 86.67065 85.66609 assigned negative charge : -773.1036 centred at (gu) : 83.74536 86.67597 85.71043 start vw surface at 0.2600000 fill in re-entrant regions at 0.2600000 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 0.5300000 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 0.6300000 number of grid points assigned charge 4988 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0336586E-14 -1.3855895E-15 midg,1,midg; midg,igrid,midg 8.7053913E-15 1.7545987E-16 1,midg,midg; igrid,midg,midg -7.1402065E-14 1.0042994E-15 gauss-seidel spectral radius is 0.9601007 estimated iterations to convergence 42 setup time was (sec) 0.7700000 now iterating at: 13:54:04 rms-change max change #iterations 1.4183932E-02 3.428551 at 10iterations 2.7362888E-03 0.8839760 at 20iterations 8.6171139E-04 0.2707214 at 30iterations 2.7387208E-04 8.3484650E-02 at 40iterations 8.7419547E-05 2.5955200E-02 at 50iterations finished qdiffx linear iterations at : 13:54:07 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 8.7419547E-05 2.5955200E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 13:54:07 3.870u 0.199s 0:04.46 91.0% 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 Mon Oct 10 2011 at 13:54:07 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5096 !!! WARNING: HIQ 363 has a net charge of 0.5140 !!! 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: 1.067648 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 : 2.135047 assigned positive charge : 775.2330 centred at (gu) : 71.36098 80.01040 76.99733 assigned negative charge : -773.1036 centred at (gu) : 71.23600 80.02782 77.13085 start vw surface at 0.2800000 fill in re-entrant regions at 0.3400000 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 = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 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 0.6700000 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 9.0716314E-04 -7.1110808E-05 midg,1,midg; midg,igrid,midg 9.5372926E-04 8.3938095E-05 1,midg,midg; igrid,midg,midg -6.4776046E-04 -2.2513630E-06 gauss-seidel spectral radius is 0.9956926 estimated iterations to convergence 122 setup time was (sec) 0.8500000 now iterating at: 13:54:08 rms-change max change #iterations 1.488359 114.0748 at 10iterations 0.3862905 20.97522 at 20iterations 0.1026100 6.366226 at 30iterations 2.8434712E-02 1.646164 at 40iterations 9.9852560E-03 0.6483994 at 50iterations 5.0199060E-03 0.2995453 at 60iterations 3.1162079E-03 0.1838646 at 70iterations 2.0413967E-03 0.1179733 at 80iterations 1.3465582E-03 7.6717377E-02 at 90iterations 8.9101901E-04 5.0167084E-02 at 100iterations 5.8952527E-04 3.2817841E-02 at 110iterations 3.9034599E-04 2.1503448E-02 at 120iterations finished qdiffx linear iterations at : 13:54:15 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 3.9034599E-04 2.1503448E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 13:54:15 7.608u 0.222s 0:08.17 95.7% 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 13:54:16 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5096 !!! WARNING: HIQ 363 has a net charge of 0.5140 !!! 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: 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 : 2.135047 assigned positive charge : 775.2330 centred at (gu) : 62.04090 75.01543 70.49548 assigned negative charge : -773.1036 centred at (gu) : 61.85397 75.04174 70.69634 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 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 = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 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 1.100000 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 6.1793845E-02 -2.7853618E-03 midg,1,midg; midg,igrid,midg 4.9687758E-02 2.5327657E-03 1,midg,midg; igrid,midg,midg -8.7998472E-02 -2.1199456E-04 gauss-seidel spectral radius is 0.9981524 estimated iterations to convergence 185 setup time was (sec) 1.310000 now iterating at: 13:54:17 rms-change max change #iterations 5.137314 184.8440 at 10iterations 2.219852 78.47829 at 20iterations 0.9491963 33.58013 at 30iterations 0.4053639 15.04819 at 40iterations 0.1710902 5.180500 at 50iterations 7.2982065E-02 2.114655 at 60iterations 3.1620905E-02 0.9824600 at 70iterations 1.4355230E-02 0.4755249 at 80iterations 7.2562494E-03 0.2553711 at 90iterations 4.3164873E-03 0.1683502 at 100iterations 2.9438881E-03 0.1016998 at 110iterations 2.1380347E-03 7.3692322E-02 at 120iterations 1.5921288E-03 5.3672791E-02 at 130iterations 1.1970380E-03 3.9657593E-02 at 140iterations 9.0243790E-04 2.9476166E-02 at 150iterations 6.8095961E-04 2.1991730E-02 at 160iterations 5.1425054E-04 1.6422272E-02 at 170iterations 3.8856789E-04 1.2271881E-02 at 180iterations finished qdiffx linear iterations at : 13:54:27 total time elapsed so far: 11.16000 # loops : 180 mean,max change (kT/e) : 3.8856789E-04 1.2271881E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 13:54:28 11.371u 0.238s 0:12.08 96.0% 0+0k 0+0io 0pf+0w