Tue Oct 11 07:50:42 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 07:50:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6366693 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): -13.76400 42.15200 ymin,ymax (A): -21.79700 30.74400 zmin,zma (A): -11.55100 40.43600 x,y,z range (A): 55.91600 52.54100 51.98700 scale (grids/A): 0.6366693 object centre (A): 14.19400 4.473499 14.44250 number of atom coordinates read : 2781 total number of charged atoms : 2416 net assigned charge : 9.500014 assigned positive charge : 388.7790 centred at (gu) : 90.25570 87.01587 90.82826 assigned negative charge : -379.2797 centred at (gu) : 90.27776 86.97633 91.01727 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6761 nv = 96 ne = 84 npr = 51562 no. pairs analyzed = 51562 no. exposed pairs = 3018 no. arc points = 21065 no. surface atoms = 1022 nbur = 1759 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3835 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3100000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2027 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6659741E-08 -8.6394101E-09 midg,1,midg; midg,igrid,midg 1.6057470E-08 9.0754719E-09 1,midg,midg; igrid,midg,midg 1.4254001E-08 1.1065413E-08 gauss-seidel spectral radius is 0.9872097 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 07:50:43 rms-change max change #iterations 0.1378429 21.08648 at 10iterations 1.3831072E-02 1.944408 at 20iterations 1.6185746E-03 0.2763901 at 30iterations 2.4207216E-04 3.3088684E-02 at 40iterations 4.9421400E-05 7.8887939E-03 at 50iterations finished qdiffx linear iterations at : 07:50:45 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 4.9421400E-05 7.8887939E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 07:50:46 3.079u 0.132s 0:03.50 91.4% 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 Tue Oct 11 2011 at 07:50:46 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.910008 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): -13.76400 42.15200 ymin,ymax (A): -21.79700 30.74400 zmin,zma (A): -11.55100 40.43600 x,y,z range (A): 55.91600 52.54100 51.98700 scale (grids/A): 1.910008 object centre (A): 14.19400 4.473499 14.44250 number of atom coordinates read : 2781 total number of charged atoms : 2416 net assigned charge : 9.500014 assigned positive charge : 388.7790 centred at (gu) : 90.76678 81.04707 92.48418 assigned negative charge : -379.2797 centred at (gu) : 90.83326 80.92883 93.05136 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 73718 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21065 grid for indexing accessible points = 1.400000 m= 27466 mr = 52067 m= 4014 mr = 20705 m= 221 mr = 2441 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 603 time to turn everything in is 0.6000000 number of dielectric boundary points 30135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18972 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) : 0.6366693 object centre at (A) : 14.19400 4.473499 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3834867E-02 -7.8254323E-03 midg,1,midg; midg,igrid,midg 1.6276322E-02 2.4691166E-02 1,midg,midg; igrid,midg,midg 1.6784044E-02 2.3196237E-02 gauss-seidel spectral radius is 0.9986266 estimated iterations to convergence 214 setup time was (sec) 0.9000000 now iterating at: 07:50:47 rms-change max change #iterations 4.205789 175.3260 at 10iterations 1.965926 69.97642 at 20iterations 0.9203963 27.81940 at 30iterations 0.4307024 13.11741 at 40iterations 0.2026369 6.719928 at 50iterations 9.4633527E-02 3.146166 at 60iterations 4.4427831E-02 1.367123 at 70iterations 2.0789769E-02 0.6609991 at 80iterations 9.7765913E-03 0.3648281 at 90iterations 4.5978311E-03 0.1647415 at 100iterations 2.1882874E-03 6.9893003E-02 at 110iterations 1.0523989E-03 3.4968853E-02 at 120iterations finished qdiffx linear iterations at : 07:50:53 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 1.0523989E-03 3.4968853E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 07:50:53 6.929u 0.180s 0:07.75 91.6% 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 Tue Oct 11 2011 at 07:50:54 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.865012 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): -13.76400 42.15200 ymin,ymax (A): -21.79700 30.74400 zmin,zma (A): -11.55100 40.43600 x,y,z range (A): 55.91600 52.54100 51.98700 scale (grids/A): 2.865012 object centre (A): 14.19400 4.473499 14.44250 number of atom coordinates read : 2781 total number of charged atoms : 2416 net assigned charge : 9.500014 assigned positive charge : 388.7790 centred at (gu) : 91.15018 76.57059 93.72628 assigned negative charge : -379.2797 centred at (gu) : 91.24976 76.39321 94.57690 start vw surface at 0.2300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 170306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21065 grid for indexing accessible points = 1.400000 m= 88853 mr = 125489 m= 32297 mr = 73973 m= 7379 mr = 26171 m= 938 mr = 5381 m= 53 mr = 631 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 2045 time to turn everything in is 1.390000 number of dielectric boundary points 68167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19326 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) : 1.910008 object centre at (A) : 14.19400 4.473499 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7137407 -0.1674827 midg,1,midg; midg,igrid,midg 0.1451659 0.2187604 1,midg,midg; igrid,midg,midg 7.1434908E-02 0.1354603 gauss-seidel spectral radius is 0.9992474 estimated iterations to convergence 288 setup time was (sec) 1.660000 now iterating at: 07:50:55 rms-change max change #iterations 9.763118 418.9800 at 10iterations 5.656577 137.0541 at 20iterations 3.262271 73.31393 at 30iterations 1.877005 37.55066 at 40iterations 1.077891 18.57691 at 50iterations 0.6187494 11.42094 at 60iterations 0.3546496 6.538155 at 70iterations 0.2033135 3.543503 at 80iterations 0.1164487 2.135177 at 90iterations 6.6681623E-02 1.367620 at 100iterations 3.8269557E-02 0.6954508 at 110iterations 2.1943990E-02 0.3911910 at 120iterations 1.2637077E-02 0.2530975 at 130iterations 7.2979438E-03 0.1372299 at 140iterations 4.2420141E-03 7.4297905E-02 at 150iterations 2.5040298E-03 4.6913147E-02 at 160iterations 1.5037643E-03 2.8266907E-02 at 170iterations 9.3668740E-04 1.7738342E-02 at 180iterations finished qdiffx linear iterations at : 07:51:05 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 9.3668740E-04 1.7738342E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 07:51:06 11.558u 0.210s 0:12.56 93.6% 0+0k 0+0io 0pf+0w