Tue Oct 11 08:28:46 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 Tue Oct 11 2011 at 08:28:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 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: 0.6585276 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): -10.30600 37.18300 ymin,ymax (A): -26.62900 21.58900 zmin,zma (A): -8.081000 45.97900 x,y,z range (A): 47.48900 48.21800 54.06000 scale (grids/A): 0.6585276 object centre (A): 13.43850 -2.520000 18.94900 number of atom coordinates read : 2820 total number of charged atoms : 2670 net assigned charge : 0.5000192 assigned positive charge : 427.3325 centred at (gu) : 89.39132 90.44997 91.42244 assigned negative charge : -426.8332 centred at (gu) : 89.09599 90.34528 91.38402 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8229 nv = 96 ne = 84 npr = 57502 no. pairs analyzed = 57502 no. exposed pairs = 3386 no. arc points = 23214 no. surface atoms = 1135 nbur = 1685 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4787 m= 6 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.3400000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8329061E-09 1.2883014E-08 midg,1,midg; midg,igrid,midg -1.8720053E-08 2.5474977E-08 1,midg,midg; igrid,midg,midg -7.0844024E-08 5.3927753E-08 gauss-seidel spectral radius is 0.9880653 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 08:28:47 rms-change max change #iterations 0.1787844 22.95327 at 10iterations 1.8816113E-02 2.410637 at 20iterations 2.0086053E-03 0.2474785 at 30iterations 2.3818601E-04 2.9312134E-02 at 40iterations 3.8689850E-05 6.6971779E-03 at 50iterations finished qdiffx linear iterations at : 08:28:50 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.8689850E-05 6.6971779E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 08:28:50 3.406u 0.147s 0:03.84 92.1% 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 Tue Oct 11 2011 at 08:28:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 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: 1.975583 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): -10.30600 37.18300 ymin,ymax (A): -26.62900 21.58900 zmin,zma (A): -8.081000 45.97900 x,y,z range (A): 47.48900 48.21800 54.06000 scale (grids/A): 1.975583 object centre (A): 13.43850 -2.520000 18.94900 number of atom coordinates read : 2820 total number of charged atoms : 2670 net assigned charge : 0.5000192 assigned positive charge : 427.3325 centred at (gu) : 88.17360 91.34927 94.26669 assigned negative charge : -426.8332 centred at (gu) : 87.28775 91.03545 94.15177 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87318 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23214 grid for indexing accessible points = 1.400000 m= 36143 mr = 62218 m= 6877 mr = 27980 m= 508 mr = 4772 m= 14 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 3352 time to turn everything in is 0.6400000 number of dielectric boundary points 35667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21065 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) : 0.6585276 object centre at (A) : 13.43850 -2.520000 18.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0723700E-02 4.9524959E-03 midg,1,midg; midg,igrid,midg -1.4883671E-02 2.7313059E-02 1,midg,midg; igrid,midg,midg -2.6765773E-02 6.2424432E-02 gauss-seidel spectral radius is 0.9987484 estimated iterations to convergence 224 setup time was (sec) 0.9300000 now iterating at: 08:28:51 rms-change max change #iterations 4.809317 193.8869 at 10iterations 2.321111 79.68377 at 20iterations 1.125134 32.87077 at 30iterations 0.5453587 15.05421 at 40iterations 0.2640983 7.770992 at 50iterations 0.1279405 3.859083 at 60iterations 6.2074024E-02 1.653782 at 70iterations 3.0014040E-02 0.8765454 at 80iterations 1.4542794E-02 0.3970490 at 90iterations 7.0534404E-03 0.1979885 at 100iterations 3.4257344E-03 9.7832680E-02 at 110iterations 1.6595443E-03 4.6346188E-02 at 120iterations finished qdiffx linear iterations at : 08:28:58 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.6595443E-03 4.6346188E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 08:28:59 7.657u 0.170s 0:08.33 93.8% 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 Tue Oct 11 2011 at 08:28:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 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: 2.963374 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): -10.30600 37.18300 ymin,ymax (A): -26.62900 21.58900 zmin,zma (A): -8.081000 45.97900 x,y,z range (A): 47.48900 48.21800 54.06000 scale (grids/A): 2.963374 object centre (A): 13.43850 -2.520000 18.94900 number of atom coordinates read : 2820 total number of charged atoms : 2670 net assigned charge : 0.5000192 assigned positive charge : 427.3325 centred at (gu) : 87.26015 92.02369 96.39996 assigned negative charge : -426.8332 centred at (gu) : 85.93146 91.55328 96.22768 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 201135 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23214 grid for indexing accessible points = 1.400000 m= 111216 mr = 149600 m= 46710 mr = 93314 m= 12970 mr = 39279 m= 2175 mr = 10201 m= 162 mr = 1571 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 11595 time to turn everything in is 1.700000 number of dielectric boundary points 80323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 21360 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) : 1.975583 object centre at (A) : 13.43850 -2.520000 18.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5216663 0.2682286 midg,1,midg; midg,igrid,midg -0.1718376 0.3167206 1,midg,midg; igrid,midg,midg -8.2410932E-02 0.5418622 gauss-seidel spectral radius is 0.9992871 estimated iterations to convergence 296 setup time was (sec) 2.010000 now iterating at: 08:29:01 rms-change max change #iterations 11.04010 398.1875 at 10iterations 6.503906 179.8307 at 20iterations 3.832449 90.52534 at 30iterations 2.249854 52.15844 at 40iterations 1.322308 25.53336 at 50iterations 0.7720124 14.81497 at 60iterations 0.4515945 7.936596 at 70iterations 0.2638480 4.760483 at 80iterations 0.1539195 2.819340 at 90iterations 8.9594536E-02 1.510752 at 100iterations 5.2281469E-02 0.8143463 at 110iterations 3.0434806E-02 0.5329237 at 120iterations 1.7715584E-02 0.2868729 at 130iterations 1.0294448E-02 0.1768284 at 140iterations 6.0079871E-03 0.1041031 at 150iterations 3.4982876E-03 5.8065891E-02 at 160iterations 2.0438395E-03 3.8392067E-02 at 170iterations 1.1978286E-03 2.0431519E-02 at 180iterations finished qdiffx linear iterations at : 08:29:12 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.1978286E-03 2.0431519E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 08:29:12 13.052u 0.214s 0:13.70 96.7% 0+0k 0+0io 0pf+0w