Mon Oct 10 17:04:47 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 17:04:47 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 = 4759 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5068842 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): -15.04400 36.66100 ymin,ymax (A): -30.08100 30.05600 zmin,zma (A): -0.3180000 69.91500 x,y,z range (A): 51.70500 60.13700 70.23300 scale (grids/A): 0.5068842 object centre (A): 10.80850 -1.2499809E-02 34.79850 number of atom coordinates read : 4759 total number of charged atoms : 4552 net assigned charge : 8.900046 assigned positive charge : 713.5405 centred at (gu) : 89.94581 91.05390 89.61459 assigned negative charge : -704.6449 centred at (gu) : 89.91488 90.99886 89.73208 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7674 nv = 96 ne = 84 npr = 96636 no. pairs analyzed = 96636 no. exposed pairs = 6039 no. arc points = 41419 no. surface atoms = 2037 nbur = 2722 mkacc time = 0.2700000 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 = 1.708000 m= 249 mr = 3927 m= 0 mr = 4 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 3992 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4042 ## 616 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 10339 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9515824E-10 -1.3997664E-10 midg,1,midg; midg,igrid,midg -1.1377595E-11 2.9578334E-10 1,midg,midg; igrid,midg,midg 3.7228397E-11 1.6920126E-10 gauss-seidel spectral radius is 0.9800937 estimated iterations to convergence 59 setup time was (sec) 0.9000000 now iterating at: 17:04:48 rms-change max change #iterations 6.4400159E-02 9.649521 at 10iterations 4.1842745E-03 0.6783562 at 20iterations 6.9693517E-04 0.1631432 at 30iterations 2.0153017E-04 4.5211792E-02 at 40iterations 6.5030137E-05 1.3050079E-02 at 50iterations finished qdiffx linear iterations at : 17:04:53 total time elapsed so far: 5.240000 # loops : 50 mean,max change (kT/e) : 6.5030137E-05 1.3050079E-02 energy calculations done at 5.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.410000 DelPhi exited at 17:04:53 5.412u 0.434s 0:06.22 93.8% 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 Mon Oct 10 2011 at 17:04:53 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 = 4759 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.520653 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): -15.04400 36.66100 ymin,ymax (A): -30.08100 30.05600 zmin,zma (A): -0.3180000 69.91500 x,y,z range (A): 51.70500 60.13700 70.23300 scale (grids/A): 1.520653 object centre (A): 10.80850 -1.2499809E-02 34.79850 number of atom coordinates read : 4759 total number of charged atoms : 4552 net assigned charge : 8.900046 assigned positive charge : 713.5405 centred at (gu) : 89.83599 93.16064 88.84234 assigned negative charge : -704.6449 centred at (gu) : 89.74440 92.99615 89.19601 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 86825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41419 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24485 mr = 59552 m= 2055 mr = 15925 m= 39 mr = 824 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 37103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 600 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 34131 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) : 0.5068842 object centre at (A) : 10.80850 -1.2499809E-02 34.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1876875E-02 7.4228796E-04 midg,1,midg; midg,igrid,midg -2.2621623E-03 -3.2040149E-03 1,midg,midg; igrid,midg,midg 1.6998861E-03 4.2122044E-03 gauss-seidel spectral radius is 0.9980793 estimated iterations to convergence 181 setup time was (sec) 1.120000 now iterating at: 17:04:55 rms-change max change #iterations 3.689960 161.1654 at 10iterations 1.500427 50.71513 at 20iterations 0.6113034 20.85163 at 30iterations 0.2473204 8.072865 at 40iterations 0.1009687 3.276901 at 50iterations 4.1301627E-02 1.577009 at 60iterations 1.6917225E-02 0.5591393 at 70iterations 7.0406348E-03 0.2295628 at 80iterations 3.0056534E-03 9.7080231E-02 at 90iterations 1.3704475E-03 5.2936554E-02 at 100iterations 6.9253461E-04 2.6216984E-02 at 110iterations 4.0055506E-04 1.4797211E-02 at 120iterations finished qdiffx linear iterations at : 17:05:05 total time elapsed so far: 11.10000 # loops : 120 mean,max change (kT/e) : 4.0055506E-04 1.4797211E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 17:05:05 11.290u 0.355s 0:12.06 96.5% 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 17:05:05 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 = 4759 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.280979 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): -15.04400 36.66100 ymin,ymax (A): -30.08100 30.05600 zmin,zma (A): -0.3180000 69.91500 x,y,z range (A): 51.70500 60.13700 70.23300 scale (grids/A): 2.280979 object centre (A): 10.80850 -1.2499809E-02 34.79850 number of atom coordinates read : 4759 total number of charged atoms : 4552 net assigned charge : 8.900046 assigned positive charge : 713.5405 centred at (gu) : 89.75379 94.74075 88.26323 assigned negative charge : -704.6449 centred at (gu) : 89.61638 94.49414 88.79397 start vw surface at 0.2200000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 202624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41419 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 88793 mr = 146827 m= 21756 mr = 68539 m= 2873 mr = 15162 m= 145 mr = 1720 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 83909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 36306 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) : 1.520653 object centre at (A) : 10.80850 -1.2499809E-02 34.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8258869 -0.1851149 midg,1,midg; midg,igrid,midg -7.1980320E-02 -0.1278394 1,midg,midg; igrid,midg,midg 2.1030223E-02 3.4445524E-02 gauss-seidel spectral radius is 0.9991542 estimated iterations to convergence 272 setup time was (sec) 2.310000 now iterating at: 17:05:08 rms-change max change #iterations 10.14393 269.8371 at 10iterations 5.843051 149.9666 at 20iterations 3.329187 97.44699 at 30iterations 1.885091 40.08498 at 40iterations 1.062345 25.02705 at 50iterations 0.5958183 11.74303 at 60iterations 0.3336205 7.957141 at 70iterations 0.1861328 3.636417 at 80iterations 0.1040653 1.931757 at 90iterations 5.7923783E-02 1.115282 at 100iterations 3.2213442E-02 0.6370583 at 110iterations 1.7871406E-02 0.3571606 at 120iterations 9.9390587E-03 0.1838779 at 130iterations 5.5185142E-03 0.1045074 at 140iterations 3.0750576E-03 5.8381796E-02 at 150iterations 1.7088150E-03 3.0769348E-02 at 160iterations 9.5463259E-04 1.7517090E-02 at 170iterations 5.3553167E-04 1.1022568E-02 at 180iterations finished qdiffx linear iterations at : 17:05:25 total time elapsed so far: 19.70000 # loops : 180 mean,max change (kT/e) : 5.3553167E-04 1.1022568E-02 energy calculations done at 19.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.88000 DelPhi exited at 17:05:26 19.880u 0.419s 0:20.60 98.4% 0+0k 0+0io 0pf+0w