Sun Oct 9 15:49:53 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 Sun Oct 9 2011 at 15:49:53 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5432 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: 0.5071008 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): -17.59700 52.60600 ymin,ymax (A): 93.83900 160.9660 zmin,zma (A): -32.28200 34.53300 x,y,z range (A): 70.20300 67.12701 66.81499 scale (grids/A): 0.5071008 object centre (A): 17.50450 127.4025 1.125500 number of atom coordinates read : 5432 total number of charged atoms : 5261 net assigned charge : 3.2767653E-05 assigned positive charge : 834.2558 centred at (gu) : 89.17367 88.40489 89.10445 assigned negative charge : -834.2630 centred at (gu) : 89.18118 88.43951 89.02476 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8584 nv = 96 ne = 84 npr = 110657 no. pairs analyzed = 110657 no. exposed pairs = 6446 no. arc points = 44924 no. surface atoms = 2154 nbur = 3278 mkacc time = 0.1800000 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 = 1.708000 m= 287 mr = 4553 m= 3 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4333 ## 650 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11641 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6593497E-10 1.6116104E-10 midg,1,midg; midg,igrid,midg 1.3840817E-10 -5.8749859E-11 1,midg,midg; igrid,midg,midg 2.4718094E-11 -1.5369227E-11 gauss-seidel spectral radius is 0.9801500 estimated iterations to convergence 59 setup time was (sec) 0.5500000 now iterating at: 15:49:54 rms-change max change #iterations 6.8580247E-02 11.77557 at 10iterations 6.3183419E-03 0.9578857 at 20iterations 2.0215940E-03 0.3509254 at 30iterations 7.8193331E-04 0.1380119 at 40iterations 3.0244087E-04 5.3783417E-02 at 50iterations finished qdiffx linear iterations at : 15:49:57 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 3.0244087E-04 5.3783417E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:49:57 3.591u 0.175s 0:04.15 90.6% 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 15:49:57 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5432 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: 1.521302 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): -17.59700 52.60600 ymin,ymax (A): 93.83900 160.9660 zmin,zma (A): -32.28200 34.53300 x,y,z range (A): 70.20300 67.12701 66.81499 scale (grids/A): 1.521302 object centre (A): 17.50450 127.4025 1.125500 number of atom coordinates read : 5432 total number of charged atoms : 5261 net assigned charge : 3.2767653E-05 assigned positive charge : 834.2558 centred at (gu) : 87.51930 85.21310 87.31149 assigned negative charge : -834.2630 centred at (gu) : 87.54312 85.31818 87.07410 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 97983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28515 mr = 68701 m= 2404 mr = 19115 m= 48 mr = 935 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 820 time to turn everything in is 0.4900000 number of dielectric boundary points 40199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 536 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 39335 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) : 0.5071008 object centre at (A) : 17.50450 127.4025 1.125500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0680237E-02 3.0753862E-03 midg,1,midg; midg,igrid,midg 1.5835345E-02 -4.6551395E-05 1,midg,midg; igrid,midg,midg -2.7264370E-02 -1.2825490E-03 gauss-seidel spectral radius is 0.9981234 estimated iterations to convergence 183 setup time was (sec) 0.7100000 now iterating at: 15:49:58 rms-change max change #iterations 4.071830 176.4080 at 10iterations 1.668105 53.42061 at 20iterations 0.6869251 20.82572 at 30iterations 0.2841737 8.785341 at 40iterations 0.1172033 3.535122 at 50iterations 4.8658207E-02 1.508308 at 60iterations 2.0719845E-02 0.6744690 at 70iterations 9.2073707E-03 0.2948647 at 80iterations 4.5145750E-03 0.1657705 at 90iterations 2.5550844E-03 9.4005585E-02 at 100iterations 1.6237503E-03 6.1374664E-02 at 110iterations 1.1055685E-03 4.2572021E-02 at 120iterations finished qdiffx linear iterations at : 15:50:05 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 1.1055685E-03 4.2572021E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 15:50:06 8.026u 0.191s 0:08.48 96.8% 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 Sun Oct 9 2011 at 15:50:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5432 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: 2.281954 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): -17.59700 52.60600 ymin,ymax (A): 93.83900 160.9660 zmin,zma (A): -32.28200 34.53300 x,y,z range (A): 70.20300 67.12701 66.81499 scale (grids/A): 2.281954 object centre (A): 17.50450 127.4025 1.125500 number of atom coordinates read : 5432 total number of charged atoms : 5261 net assigned charge : 3.2767653E-05 assigned positive charge : 834.2558 centred at (gu) : 86.27866 82.81911 85.96669 assigned negative charge : -834.2630 centred at (gu) : 86.31468 82.97716 85.61124 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 228833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 102312 mr = 168857 m= 25979 mr = 80259 m= 3409 mr = 18727 m= 169 mr = 1979 m= 4 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2927 time to turn everything in is 1.180000 number of dielectric boundary points 90848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 41988 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) : 1.521302 object centre at (A) : 17.50450 127.4025 1.125500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1735709 0.1080059 midg,1,midg; midg,igrid,midg 0.2646823 -4.2578101E-02 1,midg,midg; igrid,midg,midg -0.7035189 2.7767295E-02 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.430000 now iterating at: 15:50:08 rms-change max change #iterations 10.97243 270.4199 at 10iterations 6.285655 152.8800 at 20iterations 3.558224 96.86864 at 30iterations 2.011960 45.09015 at 40iterations 1.130897 22.97898 at 50iterations 0.6350546 12.33318 at 60iterations 0.3555878 7.176197 at 70iterations 0.1986451 3.811061 at 80iterations 0.1110667 2.067081 at 90iterations 6.2037859E-02 1.137905 at 100iterations 3.4614433E-02 0.6611812 at 110iterations 1.9320615E-02 0.3331165 at 120iterations 1.0813832E-02 0.1998291 at 130iterations 6.0852584E-03 0.1147184 at 140iterations 3.4578128E-03 6.0473442E-02 at 150iterations 2.0052465E-03 3.4721375E-02 at 160iterations 1.2065936E-03 2.4543762E-02 at 170iterations 7.6354295E-04 1.5958786E-02 at 180iterations finished qdiffx linear iterations at : 15:50:19 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 7.6354295E-04 1.5958786E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 15:50:20 13.238u 0.202s 0:13.71 97.9% 0+0k 0+0io 0pf+0w