Sat Oct 8 19:13:21 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 19:13:21 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: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6209338 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): -32.00000 18.03500 ymin,ymax (A): -24.03800 22.59700 zmin,zma (A): -12.40600 44.92700 x,y,z range (A): 50.03500 46.63500 57.33300 scale (grids/A): 0.6209338 object centre (A): -6.982500 -0.7205000 16.26050 number of atom coordinates read : 2598 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.45141 89.20629 89.82543 assigned negative charge : -388.8955 centred at (gu) : 88.33155 89.24940 89.70902 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6782 nv = 96 ne = 84 npr = 52909 no. pairs analyzed = 52909 no. exposed pairs = 3111 no. arc points = 21999 no. surface atoms = 1057 nbur = 1541 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3848 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.2900000 number of dielectric boundary points 3268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2155 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8159 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3603579E-09 1.1253563E-08 midg,1,midg; midg,igrid,midg 8.0710754E-09 7.8701368E-10 1,midg,midg; igrid,midg,midg -6.3862369E-09 8.5019263E-09 gauss-seidel spectral radius is 0.9865687 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 19:13:22 rms-change max change #iterations 0.1272187 17.01594 at 10iterations 1.1925492E-02 1.604275 at 20iterations 1.1217515E-03 0.1720924 at 30iterations 1.0826484E-04 1.5333176E-02 at 40iterations 1.1012651E-05 1.8539429E-03 at 50iterations finished qdiffx linear iterations at : 19:13:25 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.1012651E-05 1.8539429E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 19:13:25 3.302u 0.189s 0:03.77 92.3% 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 19:13:25 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: ZN5 556 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.862802 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): -32.00000 18.03500 ymin,ymax (A): -24.03800 22.59700 zmin,zma (A): -12.40600 44.92700 x,y,z range (A): 50.03500 46.63500 57.33300 scale (grids/A): 1.862802 object centre (A): -6.982500 -0.7205000 16.26050 number of atom coordinates read : 2598 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.35370 87.61845 89.47569 assigned negative charge : -388.8955 centred at (gu) : 84.99457 87.74821 89.12659 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21999 grid for indexing accessible points = 1.400000 m= 27342 mr = 50925 m= 4291 mr = 20437 m= 276 mr = 2702 m= 0 mr = 95 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2338 time to turn everything in is 0.5200000 number of dielectric boundary points 30462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19309 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) : 0.6209338 object centre at (A) : -6.982500 -0.7205000 16.26050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9091327E-02 2.7221974E-02 midg,1,midg; midg,igrid,midg 1.4653135E-02 3.3702778E-03 1,midg,midg; igrid,midg,midg -7.6066735E-03 3.8635220E-02 gauss-seidel spectral radius is 0.9985772 estimated iterations to convergence 210 setup time was (sec) 0.8100000 now iterating at: 19:13:26 rms-change max change #iterations 4.028445 155.4266 at 10iterations 1.855505 68.51162 at 20iterations 0.8550228 27.20798 at 30iterations 0.3927529 13.58759 at 40iterations 0.1814355 6.589741 at 50iterations 8.3901204E-02 2.816010 at 60iterations 3.8602497E-02 1.278639 at 70iterations 1.7806401E-02 0.5717540 at 80iterations 8.1961500E-03 0.2693214 at 90iterations 3.7909872E-03 0.1181502 at 100iterations 1.7480298E-03 5.7113647E-02 at 110iterations 8.0676738E-04 2.7262211E-02 at 120iterations finished qdiffx linear iterations at : 19:13:33 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 8.0676738E-04 2.7262211E-02 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 19:13:33 7.404u 0.234s 0:07.94 96.0% 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 19:13:33 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: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.794202 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): -32.00000 18.03500 ymin,ymax (A): -24.03800 22.59700 zmin,zma (A): -12.40600 44.92700 x,y,z range (A): 50.03500 46.63500 57.33300 scale (grids/A): 2.794202 object centre (A): -6.982500 -0.7205000 16.26050 number of atom coordinates read : 2598 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.03051 86.42750 89.21342 assigned negative charge : -388.8955 centred at (gu) : 82.49178 86.62238 88.68982 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 168092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21999 grid for indexing accessible points = 1.400000 m= 87872 mr = 122866 m= 31957 mr = 72850 m= 7715 mr = 25824 m= 1108 mr = 5824 m= 50 mr = 745 m= 0 mr = 24 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 7938 time to turn everything in is 1.290000 number of dielectric boundary points 68661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19721 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) : 1.862802 object centre at (A) : -6.982500 -0.7205000 16.26050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1285826 0.3626530 midg,1,midg; midg,igrid,midg 0.1881416 2.9506899E-02 1,midg,midg; igrid,midg,midg -5.2458480E-02 0.4854033 gauss-seidel spectral radius is 0.9992391 estimated iterations to convergence 286 setup time was (sec) 1.580000 now iterating at: 19:13:35 rms-change max change #iterations 9.497139 333.5793 at 10iterations 5.472476 115.4750 at 20iterations 3.136840 59.37622 at 30iterations 1.794012 32.95891 at 40iterations 1.024686 19.60468 at 50iterations 0.5833383 11.82830 at 60iterations 0.3333361 6.929990 at 70iterations 0.1903834 3.555931 at 80iterations 0.1084889 2.197018 at 90iterations 6.1755348E-02 1.118814 at 100iterations 3.5137273E-02 0.6948967 at 110iterations 2.0056071E-02 0.3902626 at 120iterations 1.1405439E-02 0.2228193 at 130iterations 6.5121269E-03 0.1156387 at 140iterations 3.7023267E-03 6.8737030E-02 at 150iterations 2.1128193E-03 4.1772842E-02 at 160iterations 1.2020565E-03 2.2577286E-02 at 170iterations 6.8516115E-04 1.2337685E-02 at 180iterations finished qdiffx linear iterations at : 19:13:45 total time elapsed so far: 11.96000 # loops : 180 mean,max change (kT/e) : 6.8516115E-04 1.2337685E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 19:13:46 12.147u 0.251s 0:12.67 97.7% 0+0k 0+0io 0pf+0w