Mon Oct 10 13:52:20 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 13:52:20 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 703 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6228458 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): -31.97100 17.55900 ymin,ymax (A): -23.26600 22.88700 zmin,zma (A): -12.09400 45.06300 x,y,z range (A): 49.53000 46.15300 57.15700 scale (grids/A): 0.6228458 object centre (A): -7.206000 -0.1894999 16.48450 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.73076 89.12952 89.49152 assigned negative charge : -390.0956 centred at (gu) : 88.60993 89.16708 89.37954 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6446 nv = 96 ne = 84 npr = 54243 no. pairs analyzed = 54243 no. exposed pairs = 2986 no. arc points = 21490 no. surface atoms = 1004 nbur = 1587 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3607 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.3500000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6289474E-09 1.0819299E-08 midg,1,midg; midg,igrid,midg 8.2216172E-09 1.1602969E-09 1,midg,midg; igrid,midg,midg -6.4220314E-09 9.6410986E-09 gauss-seidel spectral radius is 0.9866434 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 13:52:21 rms-change max change #iterations 0.1283261 20.23553 at 10iterations 1.1865813E-02 1.732437 at 20iterations 1.1360127E-03 0.1999350 at 30iterations 1.1263624E-04 1.5407085E-02 at 40iterations 1.2226332E-05 2.0790100E-03 at 50iterations finished qdiffx linear iterations at : 13:52:24 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.2226332E-05 2.0790100E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 13:52:25 4.092u 0.250s 0:04.68 92.7% 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 13:52:25 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 703 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.868538 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): -31.97100 17.55900 ymin,ymax (A): -23.26600 22.88700 zmin,zma (A): -12.09400 45.06300 x,y,z range (A): 49.53000 46.15300 57.15700 scale (grids/A): 1.868538 object centre (A): -7.206000 -0.1894999 16.48450 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 86.19189 87.38824 88.47362 assigned negative charge : -390.0956 centred at (gu) : 85.82956 87.50103 88.13821 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21490 grid for indexing accessible points = 1.400000 m= 24255 mr = 49012 m= 3561 mr = 17891 m= 198 mr = 2217 m= 0 mr = 79 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3926 time to turn everything in is 0.6300000 number of dielectric boundary points 29108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19320 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) : 0.6228458 object centre at (A) : -7.206000 -0.1894999 16.48450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5315218E-02 3.0861719E-02 midg,1,midg; midg,igrid,midg 1.4686149E-02 2.3767096E-03 1,midg,midg; igrid,midg,midg -9.2514940E-03 3.8106050E-02 gauss-seidel spectral radius is 0.9985765 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 13:52:26 rms-change max change #iterations 4.100648 173.6758 at 10iterations 1.887787 67.01938 at 20iterations 0.8705437 28.41982 at 30iterations 0.3993002 12.87526 at 40iterations 0.1845323 6.311675 at 50iterations 8.5329801E-02 2.715118 at 60iterations 3.9328698E-02 1.191885 at 70iterations 1.8148907E-02 0.5912933 at 80iterations 8.3405217E-03 0.2607498 at 90iterations 3.8442702E-03 0.1185856 at 100iterations 1.7781458E-03 5.8097839E-02 at 110iterations 8.1952178E-04 3.0467987E-02 at 120iterations finished qdiffx linear iterations at : 13:52:35 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 8.1952178E-04 3.0467987E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 13:52:35 9.384u 0.292s 0:10.15 95.2% 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 Mon Oct 10 2011 at 13:52:35 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 703 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.802806 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): -31.97100 17.55900 ymin,ymax (A): -23.26600 22.88700 zmin,zma (A): -12.09400 45.06300 x,y,z range (A): 49.53000 46.15300 57.15700 scale (grids/A): 2.802806 object centre (A): -7.206000 -0.1894999 16.48450 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 84.28777 86.08224 87.71017 assigned negative charge : -390.0956 centred at (gu) : 83.74432 86.25145 87.20728 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 162836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21490 grid for indexing accessible points = 1.400000 m= 79931 mr = 118695 m= 27541 mr = 65825 m= 6437 mr = 22048 m= 899 mr = 4823 m= 56 mr = 602 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 13228 time to turn everything in is 1.580000 number of dielectric boundary points 65686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 19725 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) : 1.868538 object centre at (A) : -7.206000 -0.1894999 16.48450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1195702E-02 0.4460182 midg,1,midg; midg,igrid,midg 0.1768055 6.8873307E-03 1,midg,midg; igrid,midg,midg -8.4024094E-02 0.4578036 gauss-seidel spectral radius is 0.9992369 estimated iterations to convergence 286 setup time was (sec) 1.900000 now iterating at: 13:52:37 rms-change max change #iterations 9.570667 275.9630 at 10iterations 5.486124 111.8735 at 20iterations 3.138788 62.97093 at 30iterations 1.787771 41.17248 at 40iterations 1.020904 21.15344 at 50iterations 0.5820370 11.47108 at 60iterations 0.3319716 6.968519 at 70iterations 0.1887849 3.739274 at 80iterations 0.1074397 2.064237 at 90iterations 6.1301295E-02 1.174480 at 100iterations 3.4932699E-02 0.6539011 at 110iterations 1.9845074E-02 0.3789759 at 120iterations 1.1299794E-02 0.2014503 at 130iterations 6.4412095E-03 0.1239929 at 140iterations 3.6760692E-03 6.7636490E-02 at 150iterations 2.0950981E-03 4.1003227E-02 at 160iterations 1.1944871E-03 2.2559166E-02 at 170iterations 6.8223901E-04 1.4505386E-02 at 180iterations finished qdiffx linear iterations at : 13:52:51 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 6.8223901E-04 1.4505386E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.63000 DelPhi exited at 13:52:52 15.632u 0.293s 0:16.51 96.4% 0+0k 0+0io 0pf+0w