Sat Oct 15 13:04:35 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+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 Sat Oct 15 2011 at 13:04:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5689082 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): -1.397000 51.28900 ymin,ymax (A): -7.684000 39.44700 zmin,zma (A): -15.09200 47.48400 x,y,z range (A): 52.68600 47.13100 62.57600 scale (grids/A): 0.5689082 object centre (A): 24.94600 15.88150 16.19600 number of atom coordinates read : 2679 total number of charged atoms : 2540 net assigned charge : 5.000012 assigned positive charge : 404.8624 centred at (gu) : 89.53915 90.26475 88.61592 assigned negative charge : -399.8634 centred at (gu) : 89.44956 90.13876 88.70563 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5769 nv = 96 ne = 84 npr = 53169 no. pairs analyzed = 53169 no. exposed pairs = 3433 no. arc points = 24348 no. surface atoms = 1160 nbur = 1519 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 259 mr = 2969 m= 0 mr = 11 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2476 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7299 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6856368E-09 -3.5832862E-10 midg,1,midg; midg,igrid,midg -9.5267150E-10 2.5639633E-09 1,midg,midg; igrid,midg,midg -5.7551530E-10 1.7251891E-09 gauss-seidel spectral radius is 0.9840358 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 13:04:35 rms-change max change #iterations 8.5087985E-02 13.61334 at 10iterations 6.1926544E-03 1.065834 at 20iterations 4.6745071E-04 6.5450668E-02 at 30iterations 3.8066242E-05 5.3324699E-03 at 40iterations 4.3796977E-06 7.0953369E-04 at 50iterations finished qdiffx linear iterations at : 13:04:38 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 4.3796977E-06 7.0953369E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 13:04:39 3.513u 0.177s 0:04.07 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 Sat Oct 15 2011 at 13:04:39 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 = 2679 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.706725 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): -1.397000 51.28900 ymin,ymax (A): -7.684000 39.44700 zmin,zma (A): -15.09200 47.48400 x,y,z range (A): 52.68600 47.13100 62.57600 scale (grids/A): 1.706725 object centre (A): 24.94600 15.88150 16.19600 number of atom coordinates read : 2679 total number of charged atoms : 2540 net assigned charge : 5.000012 assigned positive charge : 404.8624 centred at (gu) : 88.61642 90.79349 85.84694 assigned negative charge : -399.8634 centred at (gu) : 88.34850 90.41599 86.11649 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63537 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24348 grid for indexing accessible points = 1.400000 m= 19762 mr = 43081 m= 2112 mr = 13362 m= 64 mr = 885 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 28139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 19595 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) : 0.5689082 object centre at (A) : 24.94600 15.88150 16.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8539326E-02 4.0126457E-03 midg,1,midg; midg,igrid,midg -9.8965038E-04 6.1013168E-03 1,midg,midg; igrid,midg,midg -1.6011387E-02 5.0819847E-03 gauss-seidel spectral radius is 0.9983187 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 13:04:40 rms-change max change #iterations 3.464082 153.4188 at 10iterations 1.481370 57.32075 at 20iterations 0.6398323 23.15681 at 30iterations 0.2764809 10.18244 at 40iterations 0.1186685 4.010496 at 50iterations 5.1427662E-02 1.726155 at 60iterations 2.2038803E-02 0.7471733 at 70iterations 9.5122345E-03 0.3469801 at 80iterations 4.1009770E-03 0.1692820 at 90iterations 1.7691173E-03 6.7823410E-02 at 100iterations 7.6410035E-04 2.6672363E-02 at 110iterations 3.3039725E-04 1.1611938E-02 at 120iterations finished qdiffx linear iterations at : 13:04:47 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 3.3039725E-04 1.1611938E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:04:48 7.983u 0.231s 0:08.57 95.7% 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 15 2011 at 13:04:48 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 = 2679 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.560087 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): -1.397000 51.28900 ymin,ymax (A): -7.684000 39.44700 zmin,zma (A): -15.09200 47.48400 x,y,z range (A): 52.68600 47.13100 62.57600 scale (grids/A): 2.560087 object centre (A): 24.94600 15.88150 16.19600 number of atom coordinates read : 2679 total number of charged atoms : 2540 net assigned charge : 5.000012 assigned positive charge : 404.8624 centred at (gu) : 87.92447 91.18993 83.77032 assigned negative charge : -399.8634 centred at (gu) : 87.52267 90.62397 84.17477 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 147515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24348 grid for indexing accessible points = 1.400000 m= 68250 mr = 105454 m= 19476 mr = 53451 m= 3179 mr = 14199 m= 281 mr = 1864 m= 5 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 63625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20310 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) : 1.706725 object centre at (A) : 24.94600 15.88150 16.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6443014 5.5709556E-02 midg,1,midg; midg,igrid,midg -2.3564892E-02 1.6629087E-02 1,midg,midg; igrid,midg,midg -0.1953144 5.2884527E-02 gauss-seidel spectral radius is 0.9991730 estimated iterations to convergence 275 setup time was (sec) 1.010000 now iterating at: 13:04:49 rms-change max change #iterations 8.773665 301.5826 at 10iterations 5.040089 148.3726 at 20iterations 2.879259 87.10472 at 30iterations 1.631221 49.37177 at 40iterations 0.9230191 20.44698 at 50iterations 0.5195926 12.68172 at 60iterations 0.2921895 6.302380 at 70iterations 0.1638166 3.493038 at 80iterations 9.1731682E-02 1.971579 at 90iterations 5.1382720E-02 1.034085 at 100iterations 2.8661175E-02 0.6377993 at 110iterations 1.6013755E-02 0.3449863 at 120iterations 8.9435019E-03 0.2072334 at 130iterations 4.9975468E-03 0.1185966 at 140iterations 2.7858629E-03 5.7648182E-02 at 150iterations 1.5615521E-03 3.5552979E-02 at 160iterations 8.7745517E-04 1.8585205E-02 at 170iterations 4.9742823E-04 1.0755539E-02 at 180iterations finished qdiffx linear iterations at : 13:05:00 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 4.9742823E-04 1.0755539E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 13:05:01 12.789u 0.242s 0:13.33 97.6% 0+0k 0+0io 0pf+0w