Mon Oct 10 23:38:35 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 23:38:35 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1850 !!! WARNING: no radius record for F1 F1 2 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: 0.6585397 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): -13.89300 24.59000 ymin,ymax (A): -25.38200 16.49000 zmin,zma (A): -7.854000 46.20500 x,y,z range (A): 38.48300 41.87200 54.05900 scale (grids/A): 0.6585397 object centre (A): 5.348500 -4.446000 19.17550 number of atom coordinates read : 1850 total number of charged atoms : 1704 net assigned charge : 6.000022 assigned positive charge : 269.5193 centred at (gu) : 90.19854 90.26916 91.65672 assigned negative charge : -263.5193 centred at (gu) : 90.07328 90.27509 91.39608 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5183 nv = 96 ne = 84 npr = 38821 no. pairs analyzed = 38821 no. exposed pairs = 2244 no. arc points = 15577 no. surface atoms = 766 nbur = 1084 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 2786 m= 0 mr = 36 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3200000 number of dielectric boundary points 2644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1454 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4315367E-08 6.6355113E-08 midg,1,midg; midg,igrid,midg 1.4009776E-08 1.3986955E-08 1,midg,midg; igrid,midg,midg -2.2454458E-09 3.1247875E-08 gauss-seidel spectral radius is 0.9879762 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 23:38:36 rms-change max change #iterations 0.1369220 21.27213 at 10iterations 1.4455575E-02 2.368080 at 20iterations 1.5706160E-03 0.2522659 at 30iterations 1.8614317E-04 3.4969330E-02 at 40iterations 2.1544989E-05 3.9844513E-03 at 50iterations finished qdiffx linear iterations at : 23:38:39 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 2.1544989E-05 3.9844513E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 23:38:40 3.931u 0.164s 0:04.73 86.4% 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 23:38:40 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1850 !!! WARNING: no radius record for F1 F1 2 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.975619 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): -13.89300 24.59000 ymin,ymax (A): -25.38200 16.49000 zmin,zma (A): -7.854000 46.20500 x,y,z range (A): 38.48300 41.87200 54.05900 scale (grids/A): 1.975619 object centre (A): 5.348500 -4.446000 19.17550 number of atom coordinates read : 1850 total number of charged atoms : 1704 net assigned charge : 6.000022 assigned positive charge : 269.5193 centred at (gu) : 90.59577 90.80755 94.97064 assigned negative charge : -263.5193 centred at (gu) : 90.22002 90.82572 94.18842 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 55926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15577 grid for indexing accessible points = 1.400000 m= 19627 mr = 38421 m= 3244 mr = 14218 m= 167 mr = 2016 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1799 time to turn everything in is 0.5500000 number of dielectric boundary points 24278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 13459 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) : 0.6585397 object centre at (A) : 5.348500 -4.446000 19.17550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2559703E-03 9.8793924E-02 midg,1,midg; midg,igrid,midg -2.3942958E-03 2.7754400E-02 1,midg,midg; igrid,midg,midg 1.7721608E-03 1.2983635E-02 gauss-seidel spectral radius is 0.9986438 estimated iterations to convergence 215 setup time was (sec) 0.8700000 now iterating at: 23:38:41 rms-change max change #iterations 3.712329 169.2091 at 10iterations 1.742423 72.84007 at 20iterations 0.8181073 28.00610 at 30iterations 0.3840336 13.72699 at 40iterations 0.1799797 6.279297 at 50iterations 8.4132947E-02 3.554470 at 60iterations 3.9500240E-02 1.365131 at 70iterations 1.8563386E-02 0.6536484 at 80iterations 8.7557510E-03 0.2921982 at 90iterations 4.1271425E-03 0.1445923 at 100iterations 1.9559769E-03 6.8428040E-02 at 110iterations 9.2965440E-04 3.1761169E-02 at 120iterations finished qdiffx linear iterations at : 23:38:48 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 9.2965440E-04 3.1761169E-02 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 23:38:49 8.741u 0.208s 0:09.36 95.5% 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 23:38:49 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1850 !!! WARNING: no radius record for F1 F1 2 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: 2.963429 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): -13.89300 24.59000 ymin,ymax (A): -25.38200 16.49000 zmin,zma (A): -7.854000 46.20500 x,y,z range (A): 38.48300 41.87200 54.05900 scale (grids/A): 2.963429 object centre (A): 5.348500 -4.446000 19.17550 number of atom coordinates read : 1850 total number of charged atoms : 1704 net assigned charge : 6.000022 assigned positive charge : 269.5193 centred at (gu) : 90.89371 91.21157 97.45587 assigned negative charge : -263.5193 centred at (gu) : 90.33002 91.23863 96.28260 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 129637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15577 grid for indexing accessible points = 1.400000 m= 63148 mr = 93310 m= 23029 mr = 51184 m= 5840 mr = 18284 m= 830 mr = 4429 m= 24 mr = 497 m= 0 mr = 7 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 6188 time to turn everything in is 1.320000 number of dielectric boundary points 54797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 13632 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) : 1.975619 object centre at (A) : 5.348500 -4.446000 19.17550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3513743E-02 1.000527 midg,1,midg; midg,igrid,midg -6.5174915E-02 0.3302416 1,midg,midg; igrid,midg,midg 2.9268377E-02 8.9629091E-02 gauss-seidel spectral radius is 0.9992419 estimated iterations to convergence 287 setup time was (sec) 1.660000 now iterating at: 23:38:51 rms-change max change #iterations 8.518799 317.2738 at 10iterations 4.897355 109.8916 at 20iterations 2.816186 68.32844 at 30iterations 1.612081 37.92242 at 40iterations 0.9224441 19.42609 at 50iterations 0.5274522 11.81433 at 60iterations 0.3012664 6.665201 at 70iterations 0.1717093 3.504538 at 80iterations 9.8306850E-02 2.002449 at 90iterations 5.6197241E-02 1.311298 at 100iterations 3.2036208E-02 0.7040253 at 110iterations 1.8367987E-02 0.3874931 at 120iterations 1.0482473E-02 0.2255545 at 130iterations 6.0205604E-03 0.1207495 at 140iterations 3.4620967E-03 6.9778442E-02 at 150iterations 2.0064274E-03 4.1000366E-02 at 160iterations 1.1801596E-03 2.7587891E-02 at 170iterations 7.0793211E-04 1.7150879E-02 at 180iterations finished qdiffx linear iterations at : 23:39:03 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 7.0793211E-04 1.7150879E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 23:39:04 13.707u 0.216s 0:14.53 95.7% 0+0k 0+0io 0pf+0w