Sun Oct 9 08:57:32 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 Sun Oct 9 2011 at 08:57:32 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 = 5899 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4661455 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): 3.837000 80.20800 ymin,ymax (A): 22.53100 84.16100 zmin,zma (A): 6.315000 70.65500 x,y,z range (A): 76.37100 61.63000 64.34000 scale (grids/A): 0.4661455 object centre (A): 42.02250 53.34600 38.48500 number of atom coordinates read : 5899 total number of charged atoms : 5730 net assigned charge : -1.999959 assigned positive charge : 886.5751 centred at (gu) : 89.63489 88.87417 89.48077 assigned negative charge : -888.5829 centred at (gu) : 89.50318 88.86486 89.42605 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7824 nv = 96 ne = 84 npr = 118508 no. pairs analyzed = 118508 no. exposed pairs = 7470 no. arc points = 51959 no. surface atoms = 2494 nbur = 3405 mkacc time = 0.3200000 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 = 1.820000 m= 245 mr = 3883 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.5800000 number of dielectric boundary points 4184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4729 ## 870 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 10776 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9054868E-11 1.6333780E-11 midg,1,midg; midg,igrid,midg -9.0651722E-12 6.3537505E-13 1,midg,midg; igrid,midg,midg -6.3159006E-11 4.4180003E-11 gauss-seidel spectral radius is 0.9765704 estimated iterations to convergence 54 setup time was (sec) 0.8700000 now iterating at: 08:57:33 rms-change max change #iterations 4.6322528E-02 7.068483 at 10iterations 2.0949261E-03 0.2748134 at 20iterations 1.5638601E-04 4.0931702E-02 at 30iterations 2.9978028E-05 8.5315704E-03 at 40iterations 7.4593122E-06 1.9664764E-03 at 50iterations finished qdiffx linear iterations at : 08:57:38 total time elapsed so far: 5.450000 # loops : 50 mean,max change (kT/e) : 7.4593122E-06 1.9664764E-03 energy calculations done at 5.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.630000 DelPhi exited at 08:57:38 5.633u 0.461s 0:06.38 95.4% 0+0k 0+0io 6pf+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 Sun Oct 9 2011 at 08:57:38 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 = 5899 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.398437 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): 3.837000 80.20800 ymin,ymax (A): 22.53100 84.16100 zmin,zma (A): 6.315000 70.65500 x,y,z range (A): 76.37100 61.63000 64.34000 scale (grids/A): 1.398437 object centre (A): 42.02250 53.34600 38.48500 number of atom coordinates read : 5899 total number of charged atoms : 5730 net assigned charge : -1.999959 assigned positive charge : 886.5751 centred at (gu) : 88.90279 86.62092 88.44079 assigned negative charge : -888.5829 centred at (gu) : 88.50919 86.59412 88.27821 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 91578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51959 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 22186 mr = 61945 m= 1319 mr = 13600 m= 7 mr = 361 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 931 time to turn everything in is 0.7700000 number of dielectric boundary points 39184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 953 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 41502 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) : 0.4661455 object centre at (A) : 42.02250 53.34600 38.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8185897E-03 3.9242958E-03 midg,1,midg; midg,igrid,midg -1.1501512E-03 -2.4294308E-03 1,midg,midg; igrid,midg,midg -1.0143595E-02 1.3845403E-02 gauss-seidel spectral radius is 0.9977905 estimated iterations to convergence 169 setup time was (sec) 1.130000 now iterating at: 08:57:40 rms-change max change #iterations 3.434358 150.7028 at 10iterations 1.305728 44.62741 at 20iterations 0.5009394 16.03407 at 30iterations 0.1905556 6.753280 at 40iterations 7.2901659E-02 2.317605 at 50iterations 2.7859850E-02 0.8462181 at 60iterations 1.0642946E-02 0.3684425 at 70iterations 4.0845629E-03 0.1400681 at 80iterations 1.5697060E-03 5.3092957E-02 at 90iterations 6.0313882E-04 2.0327091E-02 at 100iterations 2.3494504E-04 9.5634460E-03 at 110iterations 9.2974311E-05 3.3569336E-03 at 120iterations finished qdiffx linear iterations at : 08:57:52 total time elapsed so far: 13.81000 # loops : 120 mean,max change (kT/e) : 9.2974311E-05 3.3569336E-03 energy calculations done at 13.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.96000 DelPhi exited at 08:57:53 13.964u 0.563s 0:14.87 97.6% 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 Sun Oct 9 2011 at 08:57:53 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 = 5899 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.097655 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): 3.837000 80.20800 ymin,ymax (A): 22.53100 84.16100 zmin,zma (A): 6.315000 70.65500 x,y,z range (A): 76.37100 61.63000 64.34000 scale (grids/A): 2.097655 object centre (A): 42.02250 53.34600 38.48500 number of atom coordinates read : 5899 total number of charged atoms : 5730 net assigned charge : -1.999959 assigned positive charge : 886.5751 centred at (gu) : 88.35394 84.93066 87.66062 assigned negative charge : -888.5829 centred at (gu) : 87.76382 84.89106 87.41735 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 214531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51959 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 85750 mr = 153933 m= 16602 mr = 64300 m= 1533 mr = 10921 m= 46 mr = 794 m= 0 mr = 7 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 3444 time to turn everything in is 1.870000 number of dielectric boundary points 88507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 45513 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) : 1.398437 object centre at (A) : 42.02250 53.34600 38.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5775336E-02 9.4154499E-02 midg,1,midg; midg,igrid,midg -1.9159105E-02 -4.1550405E-02 1,midg,midg; igrid,midg,midg -7.5854599E-02 0.2700026 gauss-seidel spectral radius is 0.9990946 estimated iterations to convergence 263 setup time was (sec) 2.350000 now iterating at: 08:57:56 rms-change max change #iterations 10.00675 309.1650 at 10iterations 5.638765 141.8203 at 20iterations 3.160343 82.18895 at 30iterations 1.758465 39.36155 at 40iterations 0.9784361 20.32925 at 50iterations 0.5392730 13.01661 at 60iterations 0.2979459 6.925228 at 70iterations 0.1637098 3.366264 at 80iterations 8.9747265E-02 2.073743 at 90iterations 4.9317542E-02 1.257453 at 100iterations 2.6921518E-02 0.5637054 at 110iterations 1.4733696E-02 0.2692719 at 120iterations 8.0405660E-03 0.1512203 at 130iterations 4.3910015E-03 8.4930420E-02 at 140iterations 2.4013717E-03 4.6656609E-02 at 150iterations 1.3072699E-03 2.6119232E-02 at 160iterations 7.1520777E-04 1.3560295E-02 at 170iterations 3.9035684E-04 7.7953339E-03 at 180iterations finished qdiffx linear iterations at : 08:58:16 total time elapsed so far: 22.32000 # loops : 180 mean,max change (kT/e) : 3.9035684E-04 7.7953339E-03 energy calculations done at 22.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.49000 DelPhi exited at 08:58:16 22.491u 0.542s 0:23.31 98.7% 0+0k 0+0io 0pf+0w