Sat Oct 8 11:40:08 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 Sat Oct 8 2011 at 11:40:08 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3376 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 567 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6571539 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): -22.98500 31.18800 ymin,ymax (A): -1.619000 51.60800 zmin,zma (A): 11.00900 59.45500 x,y,z range (A): 54.17300 53.22700 48.44600 scale (grids/A): 0.6571539 object centre (A): 4.101500 24.99450 35.23200 number of atom coordinates read : 3376 total number of charged atoms : 3248 net assigned charge : -4.499974 assigned positive charge : 517.8204 centred at (gu) : 90.58730 90.68297 89.28341 assigned negative charge : -522.3213 centred at (gu) : 90.61332 90.52231 89.40814 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9387 nv = 96 ne = 84 npr = 71770 no. pairs analyzed = 71770 no. exposed pairs = 3652 no. arc points = 24778 no. surface atoms = 1264 nbur = 2112 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 5776 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.3500000 number of dielectric boundary points 4027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2312 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11493 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2737025E-08 -3.6404604E-08 midg,1,midg; midg,igrid,midg -4.4583537E-08 3.2544786E-08 1,midg,midg; igrid,midg,midg -4.1364725E-09 -1.9746338E-08 gauss-seidel spectral radius is 0.9880515 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 11:40:09 rms-change max change #iterations 0.1987597 26.02943 at 10iterations 2.1512035E-02 2.721131 at 20iterations 2.3644755E-03 0.3343983 at 30iterations 2.7920096E-04 4.1198730E-02 at 40iterations 4.3660475E-05 7.2174072E-03 at 50iterations finished qdiffx linear iterations at : 11:40:12 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.3660475E-05 7.2174072E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:40:12 3.383u 0.195s 0:04.05 88.1% 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 Sat Oct 8 2011 at 11:40:12 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3376 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 567 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.971462 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): -22.98500 31.18800 ymin,ymax (A): -1.619000 51.60800 zmin,zma (A): 11.00900 59.45500 x,y,z range (A): 54.17300 53.22700 48.44600 scale (grids/A): 1.971462 object centre (A): 4.101500 24.99450 35.23200 number of atom coordinates read : 3376 total number of charged atoms : 3248 net assigned charge : -4.499974 assigned positive charge : 517.8204 centred at (gu) : 91.76128 92.04816 87.84932 assigned negative charge : -522.3213 centred at (gu) : 91.83936 91.56634 88.22388 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 102265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24778 grid for indexing accessible points = 1.400000 m= 38808 mr = 75506 m= 6411 mr = 30475 m= 468 mr = 4528 m= 10 mr = 216 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2752 time to turn everything in is 0.7000000 number of dielectric boundary points 37237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 25669 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) : 0.6571539 object centre at (A) : 4.101500 24.99450 35.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6073205E-03 -7.3762029E-02 midg,1,midg; midg,igrid,midg -5.0256833E-02 2.8283227E-02 1,midg,midg; igrid,midg,midg -1.0032035E-02 -2.6770562E-02 gauss-seidel spectral radius is 0.9987714 estimated iterations to convergence 226 setup time was (sec) 1.000000 now iterating at: 11:40:13 rms-change max change #iterations 5.390429 194.4936 at 10iterations 2.622200 72.23786 at 20iterations 1.276740 37.11104 at 30iterations 0.6277644 16.53601 at 40iterations 0.3056862 8.037170 at 50iterations 0.1496036 4.561676 at 60iterations 7.2992407E-02 2.582014 at 70iterations 3.5677638E-02 0.9431305 at 80iterations 1.7428134E-02 0.4972577 at 90iterations 8.5328659E-03 0.2176533 at 100iterations 4.1630361E-03 0.1025352 at 110iterations 2.0429872E-03 5.2688599E-02 at 120iterations finished qdiffx linear iterations at : 11:40:20 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.0429872E-03 5.2688599E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 11:40:21 7.776u 0.204s 0:08.31 95.9% 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 Sat Oct 8 2011 at 11:40:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3376 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 567 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.957193 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): -22.98500 31.18800 ymin,ymax (A): -1.619000 51.60800 zmin,zma (A): 11.00900 59.45500 x,y,z range (A): 54.17300 53.22700 48.44600 scale (grids/A): 2.957193 object centre (A): 4.101500 24.99450 35.23200 number of atom coordinates read : 3376 total number of charged atoms : 3248 net assigned charge : -4.499974 assigned positive charge : 517.8204 centred at (gu) : 92.64171 93.07198 86.77375 assigned negative charge : -522.3213 centred at (gu) : 92.75863 92.34930 87.33560 start vw surface at 0.1500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 236755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24778 grid for indexing accessible points = 1.400000 m= 124652 mr = 181610 m= 47200 mr = 105690 m= 12021 mr = 40162 m= 2029 mr = 9675 m= 171 mr = 1506 m= 2 mr = 101 m= 0 mr = 2 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 9139 time to turn everything in is 1.800000 number of dielectric boundary points 84084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 25984 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) : 1.971462 object centre at (A) : 4.101500 24.99450 35.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7534957E-02 -0.8251135 midg,1,midg; midg,igrid,midg -0.4591685 0.3595360 1,midg,midg; igrid,midg,midg -0.3391492 -0.2249511 gauss-seidel spectral radius is 0.9992958 estimated iterations to convergence 297 setup time was (sec) 2.110000 now iterating at: 11:40:23 rms-change max change #iterations 12.16975 352.6155 at 10iterations 7.164807 133.7728 at 20iterations 4.198164 69.92522 at 30iterations 2.467197 40.55269 at 40iterations 1.443618 23.17828 at 50iterations 0.8418462 12.94327 at 60iterations 0.4920640 8.064766 at 70iterations 0.2880466 4.567390 at 80iterations 0.1681678 2.717827 at 90iterations 9.8003864E-02 1.494910 at 100iterations 5.7121329E-02 0.8312907 at 110iterations 3.3418924E-02 0.5536261 at 120iterations 1.9462181E-02 0.2972641 at 130iterations 1.1368901E-02 0.1700239 at 140iterations 6.6526346E-03 0.1030540 at 150iterations 3.8998211E-03 6.3026428E-02 at 160iterations 2.2898994E-03 3.8142681E-02 at 170iterations 1.3553282E-03 2.0945549E-02 at 180iterations finished qdiffx linear iterations at : 11:40:34 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 1.3553282E-03 2.0945549E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 11:40:34 13.176u 0.238s 0:13.83 96.8% 0+0k 0+0io 0pf+0w