Mon Oct 10 19:32:29 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 19:32:29 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 !!! WARNING: SEP 31 has a net charge of -0.4750 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 249 has a net charge of 0.5140 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: 0.5656091 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): 40.30500 94.18200 ymin,ymax (A): -72.13200 -9.191000 zmin,zma (A): 66.79700 112.3880 x,y,z range (A): 53.87700 62.94099 45.59100 scale (grids/A): 0.5656091 object centre (A): 67.24350 -40.66150 89.59250 number of atom coordinates read : 2560 total number of charged atoms : 2418 net assigned charge : 5.3008214E-02 assigned positive charge : 391.9124 centred at (gu) : 90.08685 91.85564 90.61388 assigned negative charge : -391.8604 centred at (gu) : 90.12167 91.76411 90.76486 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5377 nv = 96 ne = 84 npr = 50961 no. pairs analyzed = 50961 no. exposed pairs = 3270 no. arc points = 22716 no. surface atoms = 1094 nbur = 1466 mkacc time = 0.1100000 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= 217 mr = 2835 m= 0 mr = 16 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2420 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6961 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5127745E-09 -2.1197568E-09 midg,1,midg; midg,igrid,midg -7.0149664E-10 1.6934661E-09 1,midg,midg; igrid,midg,midg 4.0130729E-10 -4.2416581E-10 gauss-seidel spectral radius is 0.9838376 estimated iterations to convergence 65 setup time was (sec) 0.5000000 now iterating at: 19:32:30 rms-change max change #iterations 8.1865884E-02 13.36164 at 10iterations 6.3669928E-03 1.023396 at 20iterations 6.9792964E-04 0.1395640 at 30iterations 1.3975237E-04 2.8428078E-02 at 40iterations 3.4687644E-05 7.1496964E-03 at 50iterations finished qdiffx linear iterations at : 19:32:32 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.4687644E-05 7.1496964E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 19:32:33 3.125u 0.166s 0:03.91 83.8% 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 Mon Oct 10 2011 at 19:32:33 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 !!! WARNING: SEP 31 has a net charge of -0.4750 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 249 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.696827 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): 40.30500 94.18200 ymin,ymax (A): -72.13200 -9.191000 zmin,zma (A): 66.79700 112.3880 x,y,z range (A): 53.87700 62.94099 45.59100 scale (grids/A): 1.696827 object centre (A): 67.24350 -40.66150 89.59250 number of atom coordinates read : 2560 total number of charged atoms : 2418 net assigned charge : 5.3008214E-02 assigned positive charge : 391.9124 centred at (gu) : 90.26006 95.56625 91.84075 assigned negative charge : -391.8604 centred at (gu) : 90.36471 95.29211 92.29440 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 59266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22716 grid for indexing accessible points = 1.400000 m= 19590 mr = 40637 m= 2195 mr = 13979 m= 71 mr = 1160 m= 0 mr = 13 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 463 time to turn everything in is 0.4700000 number of dielectric boundary points 25333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18681 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) : 0.5656091 object centre at (A) : 67.24350 -40.66150 89.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5885785E-03 -8.2374541E-03 midg,1,midg; midg,igrid,midg -1.0790403E-02 1.4783058E-02 1,midg,midg; igrid,midg,midg 1.5494588E-02 -5.0735269E-03 gauss-seidel spectral radius is 0.9982760 estimated iterations to convergence 191 setup time was (sec) 0.7300000 now iterating at: 19:32:34 rms-change max change #iterations 3.382526 190.9712 at 10iterations 1.432514 60.01437 at 20iterations 0.6104966 23.90512 at 30iterations 0.2607283 10.02565 at 40iterations 0.1113266 4.306644 at 50iterations 4.7476564E-02 1.703028 at 60iterations 2.0305132E-02 0.8358998 at 70iterations 8.7488033E-03 0.3310699 at 80iterations 3.8074441E-03 0.1442089 at 90iterations 1.6988172E-03 7.0550919E-02 at 100iterations 7.9210941E-04 3.0982971E-02 at 110iterations 3.9511142E-04 1.6590118E-02 at 120iterations finished qdiffx linear iterations at : 19:32:40 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 3.9511142E-04 1.6590118E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 19:32:41 6.884u 0.204s 0:08.03 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 Mon Oct 10 2011 at 19:32:41 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 !!! WARNING: SEP 31 has a net charge of -0.4750 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 249 has a net charge of 0.5140 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: 2.545241 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): 40.30500 94.18200 ymin,ymax (A): -72.13200 -9.191000 zmin,zma (A): 66.79700 112.3880 x,y,z range (A): 53.87700 62.94099 45.59100 scale (grids/A): 2.545241 object centre (A): 67.24350 -40.66150 89.59250 number of atom coordinates read : 2560 total number of charged atoms : 2418 net assigned charge : 5.3008214E-02 assigned positive charge : 391.9124 centred at (gu) : 90.38986 98.34915 92.76102 assigned negative charge : -391.8604 centred at (gu) : 90.54695 97.93816 93.44154 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 137538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22716 grid for indexing accessible points = 1.400000 m= 65832 mr = 99123 m= 20742 mr = 53042 m= 3732 mr = 16026 m= 291 mr = 2544 m= 6 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1414 time to turn everything in is 1.010000 number of dielectric boundary points 57273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 19325 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) : 1.696827 object centre at (A) : 67.24350 -40.66150 89.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0175586E-02 -8.4039219E-02 midg,1,midg; midg,igrid,midg -8.1941970E-02 0.4516810 1,midg,midg; igrid,midg,midg 0.2932685 -0.1345826 gauss-seidel spectral radius is 0.9991531 estimated iterations to convergence 271 setup time was (sec) 1.280000 now iterating at: 19:32:43 rms-change max change #iterations 8.513935 270.4401 at 10iterations 4.777777 126.8668 at 20iterations 2.673002 79.27612 at 30iterations 1.494114 34.59869 at 40iterations 0.8294128 19.06697 at 50iterations 0.4610211 10.42683 at 60iterations 0.2558032 5.454981 at 70iterations 0.1417409 3.034883 at 80iterations 7.8322694E-02 1.635625 at 90iterations 4.3393195E-02 0.9326706 at 100iterations 2.4068605E-02 0.5120354 at 110iterations 1.3292092E-02 0.2884521 at 120iterations 7.3418519E-03 0.1481705 at 130iterations 4.0740585E-03 8.9200974E-02 at 140iterations 2.2573944E-03 4.7088623E-02 at 150iterations 1.2574509E-03 2.7618408E-02 at 160iterations 7.0479483E-04 1.4730453E-02 at 170iterations 4.0084045E-04 8.9111328E-03 at 180iterations finished qdiffx linear iterations at : 19:32:52 total time elapsed so far: 10.59000 # loops : 180 mean,max change (kT/e) : 4.0084045E-04 8.9111328E-03 energy calculations done at 10.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 19:32:53 10.796u 0.225s 0:11.51 95.6% 0+0k 0+0io 0pf+0w