Sat Oct 8 18:51:30 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 18:51:30 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 496 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6309372 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): -31.84700 17.50700 ymin,ymax (A): -23.68200 22.56500 zmin,zma (A): -12.08600 44.33800 x,y,z range (A): 49.35400 46.24700 56.42400 scale (grids/A): 0.6309372 object centre (A): -7.170000 -0.5584993 16.12600 number of atom coordinates read : 2598 total number of charged atoms : 2488 net assigned charge : 4.500006 assigned positive charge : 397.2570 centred at (gu) : 88.55145 89.35922 89.85741 assigned negative charge : -392.7575 centred at (gu) : 88.45153 89.39429 89.74156 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 53165 no. pairs analyzed = 53165 no. exposed pairs = 3056 no. arc points = 21661 no. surface atoms = 1032 nbur = 1566 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3856 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.2900000 number of dielectric boundary points 3317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8362 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7680105E-09 1.5180115E-08 midg,1,midg; midg,igrid,midg 9.6125401E-09 1.7243537E-09 1,midg,midg; igrid,midg,midg -5.7650871E-09 1.0423495E-08 gauss-seidel spectral radius is 0.9869848 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 18:51:31 rms-change max change #iterations 0.1377810 21.70029 at 10iterations 1.3275824E-02 2.229919 at 20iterations 1.2522265E-03 0.1974869 at 30iterations 1.2127273E-04 1.6910553E-02 at 40iterations 1.1809304E-05 1.5306473E-03 at 50iterations finished qdiffx linear iterations at : 18:51:35 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.1809304E-05 1.5306473E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 18:51:35 4.309u 0.294s 0:04.87 94.2% 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 18:51:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 496 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.892811 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): -31.84700 17.50700 ymin,ymax (A): -23.68200 22.56500 zmin,zma (A): -12.08600 44.33800 x,y,z range (A): 49.35400 46.24700 56.42400 scale (grids/A): 1.892811 object centre (A): -7.170000 -0.5584993 16.12600 number of atom coordinates read : 2598 total number of charged atoms : 2488 net assigned charge : 4.500006 assigned positive charge : 397.2570 centred at (gu) : 85.65405 88.07725 89.57168 assigned negative charge : -392.7575 centred at (gu) : 85.35443 88.18248 89.22447 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21661 grid for indexing accessible points = 1.400000 m= 27210 mr = 52201 m= 4023 mr = 20463 m= 236 mr = 2524 m= 3 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3852 time to turn everything in is 0.5800000 number of dielectric boundary points 30476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19571 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) : 0.6309372 object centre at (A) : -7.170000 -0.5584993 16.12600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1567022E-02 3.5158973E-02 midg,1,midg; midg,igrid,midg 1.3941650E-02 1.5718587E-03 1,midg,midg; igrid,midg,midg -2.5617098E-03 4.0311590E-02 gauss-seidel spectral radius is 0.9986163 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 18:51:36 rms-change max change #iterations 4.197372 158.2224 at 10iterations 1.960723 67.93105 at 20iterations 0.9115987 30.50885 at 30iterations 0.4248305 13.44977 at 40iterations 0.1989292 6.245552 at 50iterations 9.2743702E-02 2.835289 at 60iterations 4.3201979E-02 1.481045 at 70iterations 2.0169612E-02 0.6635419 at 80iterations 9.3792211E-03 0.2990379 at 90iterations 4.3873680E-03 0.1354580 at 100iterations 2.0536410E-03 6.2676907E-02 at 110iterations 9.5562247E-04 3.3453465E-02 at 120iterations finished qdiffx linear iterations at : 18:51:45 total time elapsed so far: 9.820000 # loops : 120 mean,max change (kT/e) : 9.5562247E-04 3.3453465E-02 energy calculations done at 9.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 18:51:46 9.999u 0.312s 0:10.57 97.4% 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 Sat Oct 8 2011 at 18:51:46 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 496 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.839217 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): -31.84700 17.50700 ymin,ymax (A): -23.68200 22.56500 zmin,zma (A): -12.08600 44.33800 x,y,z range (A): 49.35400 46.24700 56.42400 scale (grids/A): 2.839217 object centre (A): -7.170000 -0.5584993 16.12600 number of atom coordinates read : 2598 total number of charged atoms : 2488 net assigned charge : 4.500006 assigned positive charge : 397.2570 centred at (gu) : 83.48088 87.11562 89.35739 assigned negative charge : -392.7575 centred at (gu) : 83.03171 87.27356 88.83664 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 171825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21661 grid for indexing accessible points = 1.400000 m= 88432 mr = 126095 m= 31589 mr = 73374 m= 7127 mr = 25546 m= 962 mr = 5436 m= 74 mr = 712 m= 0 mr = 31 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 12964 time to turn everything in is 1.450000 number of dielectric boundary points 68815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 19904 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) : 1.892811 object centre at (A) : -7.170000 -0.5584993 16.12600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1618148 0.4008884 midg,1,midg; midg,igrid,midg 0.1664567 5.4369816E-03 1,midg,midg; igrid,midg,midg 1.9912923E-02 0.5207276 gauss-seidel spectral radius is 0.9992487 estimated iterations to convergence 288 setup time was (sec) 1.830000 now iterating at: 18:51:48 rms-change max change #iterations 9.861181 374.2283 at 10iterations 5.717780 162.3177 at 20iterations 3.281443 71.81778 at 30iterations 1.884664 42.74777 at 40iterations 1.082208 21.73120 at 50iterations 0.6194651 11.53075 at 60iterations 0.3556521 7.142369 at 70iterations 0.2034074 4.714444 at 80iterations 0.1162188 2.177588 at 90iterations 6.6664286E-02 1.238892 at 100iterations 3.8127054E-02 0.7197990 at 110iterations 2.1792874E-02 0.4069366 at 120iterations 1.2502151E-02 0.2198353 at 130iterations 7.1460903E-03 0.1379032 at 140iterations 4.0833959E-03 7.5752258E-02 at 150iterations 2.3343258E-03 4.4110298E-02 at 160iterations 1.3334987E-03 2.4644852E-02 at 170iterations 7.6382654E-04 1.3709068E-02 at 180iterations finished qdiffx linear iterations at : 18:52:02 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 7.6382654E-04 1.3709068E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.24000 DelPhi exited at 18:52:03 16.241u 0.334s 0:16.84 98.3% 0+0k 0+0io 0pf+0w