Mon Oct 10 14:07:11 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 14:07:11 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 = 2574 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: 0.6579555 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): -9.246000 44.86100 ymin,ymax (A): -18.27700 30.15800 zmin,zma (A): 17.83500 70.78300 x,y,z range (A): 54.10700 48.43500 52.94800 scale (grids/A): 0.6579555 object centre (A): 17.80750 5.940499 44.30900 number of atom coordinates read : 2574 total number of charged atoms : 2425 net assigned charge : -12.49998 assigned positive charge : 390.9292 centred at (gu) : 88.28642 88.43665 90.18250 assigned negative charge : -403.4295 centred at (gu) : 88.29474 88.24390 90.00368 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7729 nv = 96 ne = 84 npr = 50736 no. pairs analyzed = 50736 no. exposed pairs = 3574 no. arc points = 25574 no. surface atoms = 1183 nbur = 1391 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3971 m= 0 mr = 32 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 107 time to turn everything in is 0.3000000 number of dielectric boundary points 4156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8847 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2204876E-08 5.0090061E-09 midg,1,midg; midg,igrid,midg -9.3596761E-08 4.9020863E-09 1,midg,midg; igrid,midg,midg -3.9102090E-08 -2.1939565E-08 gauss-seidel spectral radius is 0.9880379 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 14:07:12 rms-change max change #iterations 0.1687747 26.79314 at 10iterations 1.7879514E-02 2.428730 at 20iterations 1.8945120E-03 0.2447329 at 30iterations 2.2674011E-04 2.8691530E-02 at 40iterations 3.6909831E-05 4.6405792E-03 at 50iterations finished qdiffx linear iterations at : 14:07:14 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 3.6909831E-05 4.6405792E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 14:07:15 3.191u 0.142s 0:03.68 90.4% 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 14:07:15 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 = 2574 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: 1.973866 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): -9.246000 44.86100 ymin,ymax (A): -18.27700 30.15800 zmin,zma (A): 17.83500 70.78300 x,y,z range (A): 54.10700 48.43500 52.94800 scale (grids/A): 1.973866 object centre (A): 17.80750 5.940499 44.30900 number of atom coordinates read : 2574 total number of charged atoms : 2425 net assigned charge : -12.49998 assigned positive charge : 390.9292 centred at (gu) : 84.85892 85.30959 90.54684 assigned negative charge : -403.4295 centred at (gu) : 84.88410 84.73132 90.01079 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25574 grid for indexing accessible points = 1.400000 m= 30026 mr = 54079 m= 4785 mr = 21441 m= 344 mr = 2757 m= 5 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 3004 time to turn everything in is 0.5600000 number of dielectric boundary points 38483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19165 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) : 0.6579555 object centre at (A) : 17.80750 5.940499 44.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3072587E-02 -5.4916888E-03 midg,1,midg; midg,igrid,midg -9.2790611E-02 1.4972943E-02 1,midg,midg; igrid,midg,midg -2.9389694E-02 -4.5192719E-02 gauss-seidel spectral radius is 0.9987403 estimated iterations to convergence 223 setup time was (sec) 0.8300000 now iterating at: 14:07:16 rms-change max change #iterations 4.617856 233.2984 at 10iterations 2.226591 72.57779 at 20iterations 1.066517 33.31112 at 30iterations 0.5143832 17.64291 at 40iterations 0.2477966 7.431129 at 50iterations 0.1194556 3.608063 at 60iterations 5.7497118E-02 1.738900 at 70iterations 2.7630417E-02 0.7958832 at 80iterations 1.3392673E-02 0.4221230 at 90iterations 6.4514680E-03 0.1967757 at 100iterations 3.1146219E-03 9.5283508E-02 at 110iterations 1.5028539E-03 4.7997475E-02 at 120iterations finished qdiffx linear iterations at : 14:07:22 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 1.5028539E-03 4.7997475E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 14:07:23 7.241u 0.202s 0:07.81 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 14:07:23 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 = 2574 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.960800 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): -9.246000 44.86100 ymin,ymax (A): -18.27700 30.15800 zmin,zma (A): 17.83500 70.78300 x,y,z range (A): 54.10700 48.43500 52.94800 scale (grids/A): 2.960800 object centre (A): 17.80750 5.940499 44.30900 number of atom coordinates read : 2574 total number of charged atoms : 2425 net assigned charge : -12.49998 assigned positive charge : 390.9292 centred at (gu) : 82.28823 82.96442 90.82004 assigned negative charge : -403.4295 centred at (gu) : 82.32606 82.09694 90.01618 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 188410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25574 grid for indexing accessible points = 1.400000 m= 95041 mr = 131228 m= 35644 mr = 76237 m= 8544 mr = 27764 m= 1252 mr = 6044 m= 118 mr = 821 m= 5 mr = 49 m= 0 mr = 2 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 10199 time to turn everything in is 1.420000 number of dielectric boundary points 86869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 19399 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) : 1.973866 object centre at (A) : 17.80750 5.940499 44.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6118307 -8.2334250E-02 midg,1,midg; midg,igrid,midg -1.003860 0.2332128 1,midg,midg; igrid,midg,midg -0.2452194 -0.4185391 gauss-seidel spectral radius is 0.9993020 estimated iterations to convergence 299 setup time was (sec) 1.710000 now iterating at: 14:07:25 rms-change max change #iterations 10.87852 462.8335 at 10iterations 6.478090 144.7642 at 20iterations 3.842121 85.56809 at 30iterations 2.271235 48.94213 at 40iterations 1.342953 31.31895 at 50iterations 0.7904773 16.30430 at 60iterations 0.4658046 9.018873 at 70iterations 0.2736286 4.858358 at 80iterations 0.1606300 2.768984 at 90iterations 9.4344661E-02 2.060814 at 100iterations 5.5264585E-02 1.090191 at 110iterations 3.2369349E-02 0.5436420 at 120iterations 1.8937889E-02 0.3595896 at 130iterations 1.1094954E-02 0.2141037 at 140iterations 6.5011196E-03 0.1153731 at 150iterations 3.7972268E-03 6.4678192E-02 at 160iterations 2.2245874E-03 4.0167570E-02 at 170iterations 1.3043346E-03 2.3458481E-02 at 180iterations finished qdiffx linear iterations at : 14:07:35 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.3043346E-03 2.3458481E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 14:07:36 11.647u 0.194s 0:12.47 94.8% 0+0k 0+0io 0pf+0w