Tue Oct 11 05:13:36 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 05:13:36 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 = 2064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7090080 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): -19.75300 26.49500 ymin,ymax (A): -10.73400 28.40300 zmin,zma (A): -2.631000 47.58000 x,y,z range (A): 46.24800 39.13700 50.21100 scale (grids/A): 0.7090080 object centre (A): 3.370999 8.834500 22.47450 number of atom coordinates read : 2064 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 89.27266 89.25378 90.11328 assigned negative charge : -307.4362 centred at (gu) : 89.14787 89.27337 90.16236 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7022 nv = 96 ne = 84 npr = 41425 no. pairs analyzed = 41425 no. exposed pairs = 2565 no. arc points = 17122 no. surface atoms = 876 nbur = 1188 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4051 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1561 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7740 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0242728E-08 3.3175610E-08 midg,1,midg; midg,igrid,midg 7.7479378E-08 4.1379877E-08 1,midg,midg; igrid,midg,midg -7.8959808E-09 1.0387272E-07 gauss-seidel spectral radius is 0.9896266 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 05:13:37 rms-change max change #iterations 0.2019932 28.90836 at 10iterations 2.5214041E-02 3.133659 at 20iterations 3.2392966E-03 0.4874535 at 30iterations 4.8608280E-04 7.7530861E-02 at 40iterations 9.9762357E-05 1.2282372E-02 at 50iterations finished qdiffx linear iterations at : 05:13:40 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 9.9762357E-05 1.2282372E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 05:13:41 4.079u 0.266s 0:04.97 87.1% 0+0k 0+0io 5pf+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 05:13:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.127024 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): -19.75300 26.49500 ymin,ymax (A): -10.73400 28.40300 zmin,zma (A): -2.631000 47.58000 x,y,z range (A): 46.24800 39.13700 50.21100 scale (grids/A): 2.127024 object centre (A): 3.370999 8.834500 22.47450 number of atom coordinates read : 2064 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 87.81795 87.76142 90.33971 assigned negative charge : -307.4362 centred at (gu) : 87.44366 87.82005 90.48714 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17122 grid for indexing accessible points = 1.400000 m= 29818 mr = 52848 m= 5700 mr = 22661 m= 533 mr = 3847 m= 14 mr = 238 m= 0 mr = 3 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 30759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15385 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) : 0.7090080 object centre at (A) : 3.370999 8.834500 22.47450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1044470E-02 5.8922730E-02 midg,1,midg; midg,igrid,midg 3.4878954E-02 7.7850455E-03 1,midg,midg; igrid,midg,midg 7.8492528E-03 3.2507814E-02 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.9700000 now iterating at: 05:13:42 rms-change max change #iterations 4.600737 180.7353 at 10iterations 2.288465 81.77389 at 20iterations 1.135844 38.33426 at 30iterations 0.5640734 18.99966 at 40iterations 0.2812341 8.191223 at 50iterations 0.1389778 4.505478 at 60iterations 6.9058880E-02 2.039134 at 70iterations 3.4391075E-02 1.152011 at 80iterations 1.7166186E-02 0.5651417 at 90iterations 8.5629858E-03 0.2650299 at 100iterations 4.2952299E-03 0.1447923 at 110iterations 2.1821377E-03 6.2585831E-02 at 120iterations finished qdiffx linear iterations at : 05:13:50 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 2.1821377E-03 6.2585831E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 05:13:52 9.595u 0.339s 0:11.79 84.1% 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 Tue Oct 11 2011 at 05:13:53 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 = 2064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.190536 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): -19.75300 26.49500 ymin,ymax (A): -10.73400 28.40300 zmin,zma (A): -2.631000 47.58000 x,y,z range (A): 46.24800 39.13700 50.21100 scale (grids/A): 3.190536 object centre (A): 3.370999 8.834500 22.47450 number of atom coordinates read : 2064 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 86.72686 86.64188 90.50967 assigned negative charge : -307.4362 centred at (gu) : 86.16549 86.73007 90.73077 start vw surface at 0.1400000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 171324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17122 grid for indexing accessible points = 1.400000 m= 92849 mr = 127371 m= 37740 mr = 77241 m= 10908 mr = 31113 m= 2048 mr = 8398 m= 203 mr = 1485 m= 6 mr = 125 m= 0 mr = 3 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.190000 number of dielectric boundary points 69342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15488 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) : 2.127024 object centre at (A) : 3.370999 8.834500 22.47450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3657157 0.9556071 midg,1,midg; midg,igrid,midg 0.2809081 3.2889143E-02 1,midg,midg; igrid,midg,midg 0.1705710 0.2648715 gauss-seidel spectral radius is 0.9992939 estimated iterations to convergence 297 setup time was (sec) 2.530000 now iterating at: 05:13:56 rms-change max change #iterations 10.22056 380.6768 at 10iterations 6.051420 128.1028 at 20iterations 3.556008 76.38483 at 30iterations 2.090849 41.68348 at 40iterations 1.227023 21.46480 at 50iterations 0.7222278 14.73836 at 60iterations 0.4230456 8.612106 at 70iterations 0.2476079 4.247086 at 80iterations 0.1447164 2.701179 at 90iterations 8.4877551E-02 1.558829 at 100iterations 4.9635567E-02 0.8986282 at 110iterations 2.9109277E-02 0.5302811 at 120iterations 1.7197387E-02 0.2851629 at 130iterations 1.0226876E-02 0.1915016 at 140iterations 6.2112138E-03 0.1384544 at 150iterations 3.8552955E-03 7.1929932E-02 at 160iterations 2.5145146E-03 4.5394897E-02 at 170iterations 1.7303854E-03 3.6029816E-02 at 180iterations finished qdiffx linear iterations at : 05:14:10 total time elapsed so far: 16.41000 # loops : 180 mean,max change (kT/e) : 1.7303854E-03 3.6029816E-02 energy calculations done at 16.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.58000 DelPhi exited at 05:14:10 16.585u 0.316s 0:17.45 96.7% 0+0k 0+0io 0pf+0w