Mon Oct 10 14:01:21 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 14:01:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 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: 0.6283424 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): 45.55300 102.2100 ymin,ymax (A): -24.65000 28.71400 zmin,zma (A): 1.883000 53.72200 x,y,z range (A): 56.65700 53.36400 51.83900 scale (grids/A): 0.6283424 object centre (A): 73.88150 2.032000 27.80250 number of atom coordinates read : 3277 total number of charged atoms : 3130 net assigned charge : 2.500007 assigned positive charge : 490.2646 centred at (gu) : 88.95850 88.55349 90.04970 assigned negative charge : -487.7661 centred at (gu) : 88.86722 88.56987 90.09460 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8477 nv = 96 ne = 84 npr = 68347 no. pairs analyzed = 68347 no. exposed pairs = 3663 no. arc points = 25682 no. surface atoms = 1254 nbur = 2023 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4916 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.4000000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2501 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3173445E-09 -2.1242907E-09 midg,1,midg; midg,igrid,midg 6.0228782E-09 7.1368522E-10 1,midg,midg; igrid,midg,midg -8.9737986E-09 9.7444195E-09 gauss-seidel spectral radius is 0.9869324 estimated iterations to convergence 72 setup time was (sec) 0.6800000 now iterating at: 14:01:39 rms-change max change #iterations 0.1511493 19.58750 at 10iterations 1.4886565E-02 1.889008 at 20iterations 1.5319050E-03 0.2116985 at 30iterations 1.9274339E-04 2.4999619E-02 at 40iterations 3.5727506E-05 4.0734410E-03 at 50iterations finished qdiffx linear iterations at : 14:01:44 total time elapsed so far: 4.970000 # loops : 50 mean,max change (kT/e) : 3.5727506E-05 4.0734410E-03 energy calculations done at 4.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 14:01:44 5.129u 0.515s 0:23.76 23.6% 0+0k 0+0io 6pf+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 14:01:45 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 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: 1.885027 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): 45.55300 102.2100 ymin,ymax (A): -24.65000 28.71400 zmin,zma (A): 1.883000 53.72200 x,y,z range (A): 56.65700 53.36400 51.83900 scale (grids/A): 1.885027 object centre (A): 73.88150 2.032000 27.80250 number of atom coordinates read : 3277 total number of charged atoms : 3130 net assigned charge : 2.500007 assigned positive charge : 490.2646 centred at (gu) : 86.87486 85.65976 90.14851 assigned negative charge : -487.7661 centred at (gu) : 86.60129 85.70929 90.28362 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 92977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25682 grid for indexing accessible points = 1.400000 m= 33581 mr = 67176 m= 4940 mr = 25128 m= 265 mr = 3045 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1112 time to turn everything in is 0.7500000 number of dielectric boundary points 36345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24628 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) : 0.6283424 object centre at (A) : 73.88150 2.032000 27.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3092290E-02 -1.3465844E-02 midg,1,midg; midg,igrid,midg 8.8833151E-03 7.4873357E-03 1,midg,midg; igrid,midg,midg -1.1223309E-03 4.0499810E-02 gauss-seidel spectral radius is 0.9986633 estimated iterations to convergence 217 setup time was (sec) 1.110000 now iterating at: 14:01:46 rms-change max change #iterations 4.709258 173.2912 at 10iterations 2.222334 67.32126 at 20iterations 1.049047 31.56546 at 30iterations 0.4960789 15.51352 at 40iterations 0.2350531 6.441472 at 50iterations 0.1113154 3.163475 at 60iterations 5.2486315E-02 1.481995 at 70iterations 2.4818260E-02 0.7277985 at 80iterations 1.1775565E-02 0.3285580 at 90iterations 5.5728904E-03 0.1594610 at 100iterations 2.6342336E-03 8.2527161E-02 at 110iterations 1.2526764E-03 3.6668777E-02 at 120iterations finished qdiffx linear iterations at : 14:01:58 total time elapsed so far: 12.41000 # loops : 120 mean,max change (kT/e) : 1.2526764E-03 3.6668777E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 14:01:58 12.585u 0.534s 0:13.56 96.6% 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 14:01:58 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.827541 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): 45.55300 102.2100 ymin,ymax (A): -24.65000 28.71400 zmin,zma (A): 1.883000 53.72200 x,y,z range (A): 56.65700 53.36400 51.83900 scale (grids/A): 2.827541 object centre (A): 73.88150 2.032000 27.80250 number of atom coordinates read : 3277 total number of charged atoms : 3130 net assigned charge : 2.500007 assigned positive charge : 490.2646 centred at (gu) : 85.31207 83.48949 90.22241 assigned negative charge : -487.7661 centred at (gu) : 84.90198 83.56385 90.42540 start vw surface at 0.1300000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 215412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25682 grid for indexing accessible points = 1.400000 m= 110072 mr = 162031 m= 38859 mr = 91533 m= 8723 mr = 31350 m= 1072 mr = 6500 m= 49 mr = 690 m= 0 mr = 11 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 3600 time to turn everything in is 2.010000 number of dielectric boundary points 82072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 25037 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) : 1.885027 object centre at (A) : 73.88150 2.032000 27.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3276708 -0.1190284 midg,1,midg; midg,igrid,midg -0.1716299 6.0079668E-02 1,midg,midg; igrid,midg,midg 3.6671847E-02 0.4628173 gauss-seidel spectral radius is 0.9992741 estimated iterations to convergence 293 setup time was (sec) 2.420000 now iterating at: 14:02:01 rms-change max change #iterations 11.05955 428.9811 at 10iterations 6.466935 162.7128 at 20iterations 3.765193 67.01092 at 30iterations 2.193304 38.37255 at 40iterations 1.271625 25.48077 at 50iterations 0.7372428 13.25671 at 60iterations 0.4273174 7.261662 at 70iterations 0.2470737 3.978590 at 80iterations 0.1433207 2.368458 at 90iterations 8.2749337E-02 1.520582 at 100iterations 4.7920298E-02 0.8565025 at 110iterations 2.7718542E-02 0.4494658 at 120iterations 1.6048916E-02 0.2619743 at 130iterations 9.3285115E-03 0.1511116 at 140iterations 5.4088198E-03 8.3287239E-02 at 150iterations 3.1581598E-03 4.9461365E-02 at 160iterations 1.8519437E-03 2.8856754E-02 at 170iterations 1.0961257E-03 1.8310547E-02 at 180iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 21.22000 # loops : 180 mean,max change (kT/e) : 1.0961257E-03 1.8310547E-02 energy calculations done at 21.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.39000 DelPhi exited at 14:02:21 21.397u 0.530s 0:22.74 96.3% 0+0k 0+0io 0pf+0w