Sat Oct 8 13:29:48 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 Sat Oct 8 2011 at 13:29:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 631 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6195830 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): -54.04800 -0.6569999 ymin,ymax (A): -18.98200 38.47600 zmin,zma (A): -66.57300 -19.81400 x,y,z range (A): 53.39100 57.45800 46.75900 scale (grids/A): 0.6195830 object centre (A): -27.35250 9.747001 -43.19350 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0725 centred at (gu) : 90.99702 91.53049 89.98680 assigned negative charge : -454.0733 centred at (gu) : 90.99126 91.43238 89.93720 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7571 nv = 96 ne = 84 npr = 64440 no. pairs analyzed = 64440 no. exposed pairs = 3511 no. arc points = 23688 no. surface atoms = 1193 nbur = 1838 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 4443 m= 0 mr = 27 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3400000 number of dielectric boundary points 3461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2239 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9614503E-09 3.6386905E-09 midg,1,midg; midg,igrid,midg -5.4958060E-09 1.0335257E-08 1,midg,midg; igrid,midg,midg -4.5659529E-10 3.9088113E-10 gauss-seidel spectral radius is 0.9865369 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 13:29:49 rms-change max change #iterations 0.1397192 19.27901 at 10iterations 1.3457659E-02 1.841888 at 20iterations 1.4657861E-03 0.1928358 at 30iterations 2.5276392E-04 4.2560577E-02 at 40iterations 5.9025471E-05 9.6111298E-03 at 50iterations finished qdiffx linear iterations at : 13:29:52 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 5.9025471E-05 9.6111298E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 13:29:53 4.458u 0.398s 0:05.11 94.7% 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 Sat Oct 8 2011 at 13:29:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 631 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.858749 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): -54.04800 -0.6569999 ymin,ymax (A): -18.98200 38.47600 zmin,zma (A): -66.57300 -19.81400 x,y,z range (A): 53.39100 57.45800 46.75900 scale (grids/A): 1.858749 object centre (A): -27.35250 9.747001 -43.19350 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0725 centred at (gu) : 92.99063 94.59089 89.95989 assigned negative charge : -454.0733 centred at (gu) : 92.97359 94.29668 89.81123 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23688 grid for indexing accessible points = 1.400000 m= 29523 mr = 59476 m= 3934 mr = 22047 m= 152 mr = 2276 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 32199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22622 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) : 0.6195830 object centre at (A) : -27.35250 9.747001 -43.19350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6233629E-03 1.8416414E-03 midg,1,midg; midg,igrid,midg -2.3314254E-02 2.2251496E-02 1,midg,midg; igrid,midg,midg -3.4161878E-03 -2.4380928E-02 gauss-seidel spectral radius is 0.9986002 estimated iterations to convergence 212 setup time was (sec) 0.9500000 now iterating at: 13:29:54 rms-change max change #iterations 4.415421 173.2913 at 10iterations 2.047205 64.75496 at 20iterations 0.9525186 28.32941 at 30iterations 0.4409774 17.21924 at 40iterations 0.2063673 6.000435 at 50iterations 9.5467679E-02 2.685769 at 60iterations 4.4489134E-02 1.366558 at 70iterations 2.0754451E-02 0.5904932 at 80iterations 9.7130295E-03 0.3427048 at 90iterations 4.5650778E-03 0.1673393 at 100iterations 2.1556460E-03 6.3810349E-02 at 110iterations 1.0286879E-03 3.3309937E-02 at 120iterations finished qdiffx linear iterations at : 13:30:04 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.0286879E-03 3.3309937E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 13:30:04 10.562u 0.449s 0:11.28 97.5% 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 Sat Oct 8 2011 at 13:30:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 631 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.788124 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): -54.04800 -0.6569999 ymin,ymax (A): -18.98200 38.47600 zmin,zma (A): -66.57300 -19.81400 x,y,z range (A): 53.39100 57.45800 46.75900 scale (grids/A): 2.788124 object centre (A): -27.35250 9.747001 -43.19350 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0725 centred at (gu) : 94.48586 96.88624 89.93959 assigned negative charge : -454.0733 centred at (gu) : 94.46042 96.44496 89.71684 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 190887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23688 grid for indexing accessible points = 1.400000 m= 96992 mr = 143718 m= 33314 mr = 80450 m= 6776 mr = 26731 m= 700 mr = 4840 m= 36 mr = 385 m= 0 mr = 7 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.730000 number of dielectric boundary points 72574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 23071 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) : 1.858749 object centre at (A) : -27.35250 9.747001 -43.19350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7194262E-02 4.9187306E-02 midg,1,midg; midg,igrid,midg -0.1740035 0.2944447 1,midg,midg; igrid,midg,midg -0.1965215 -0.3530089 gauss-seidel spectral radius is 0.9992529 estimated iterations to convergence 289 setup time was (sec) 2.050000 now iterating at: 13:30:07 rms-change max change #iterations 10.47071 311.0280 at 10iterations 6.122878 140.1287 at 20iterations 3.551563 78.44559 at 30iterations 2.056481 39.69035 at 40iterations 1.189613 23.02933 at 50iterations 0.6850746 12.02796 at 60iterations 0.3938937 7.809283 at 70iterations 0.2267119 3.965656 at 80iterations 0.1306194 2.378203 at 90iterations 7.5090975E-02 1.334450 at 100iterations 4.3142378E-02 0.7493100 at 110iterations 2.4747409E-02 0.4485052 at 120iterations 1.4202311E-02 0.2470045 at 130iterations 8.1912875E-03 0.1417627 at 140iterations 4.7138133E-03 7.7346802E-02 at 150iterations 2.7194915E-03 5.0533295E-02 at 160iterations 1.5826327E-03 2.7900696E-02 at 170iterations 9.2849892E-04 1.7545700E-02 at 180iterations finished qdiffx linear iterations at : 13:30:23 total time elapsed so far: 17.84000 # loops : 180 mean,max change (kT/e) : 9.2849892E-04 1.7545700E-02 energy calculations done at 17.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.02000 DelPhi exited at 13:30:23 18.029u 0.473s 0:18.76 98.5% 0+0k 0+0io 0pf+0w