Mon Oct 10 14:00:18 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 Mon Oct 10 2011 at 14:00:18 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3065 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: 0.6010569 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): -18.77500 36.70400 ymin,ymax (A): -21.41100 37.81800 zmin,zma (A): 3.935000 60.55700 x,y,z range (A): 55.47900 59.22900 56.62200 scale (grids/A): 0.6010569 object centre (A): 8.964501 8.203499 32.24600 number of atom coordinates read : 3065 total number of charged atoms : 2928 net assigned charge : -2.499991 assigned positive charge : 467.0289 centred at (gu) : 88.47372 90.31210 87.99224 assigned negative charge : -469.5301 centred at (gu) : 88.46091 90.44107 88.07256 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7374 nv = 96 ne = 84 npr = 62726 no. pairs analyzed = 62726 no. exposed pairs = 3880 no. arc points = 27583 no. surface atoms = 1304 nbur = 1761 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 3944 m= 3 mr = 61 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2300000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2768 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9694399E-09 -3.0634115E-09 midg,1,midg; midg,igrid,midg 4.2842014E-09 -7.6000966E-09 1,midg,midg; igrid,midg,midg -2.4370559E-09 -4.1406178E-10 gauss-seidel spectral radius is 0.9857165 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 14:00:18 rms-change max change #iterations 0.1254411 19.48160 at 10iterations 1.1092992E-02 1.473000 at 20iterations 1.0361765E-03 0.1423218 at 30iterations 1.4884993E-04 2.1430969E-02 at 40iterations 3.2141059E-05 5.1593781E-03 at 50iterations finished qdiffx linear iterations at : 14:00:21 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.2141059E-05 5.1593781E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:00:22 3.448u 0.172s 0:04.15 86.9% 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 Mon Oct 10 2011 at 14:00:22 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3065 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: 1.803171 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): -18.77500 36.70400 ymin,ymax (A): -21.41100 37.81800 zmin,zma (A): 3.935000 60.55700 x,y,z range (A): 55.47900 59.22900 56.62200 scale (grids/A): 1.803171 object centre (A): 8.964501 8.203499 32.24600 number of atom coordinates read : 3065 total number of charged atoms : 2928 net assigned charge : -2.499991 assigned positive charge : 467.0289 centred at (gu) : 85.42016 90.93530 83.97562 assigned negative charge : -469.5301 centred at (gu) : 85.38236 91.32277 84.21748 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27583 grid for indexing accessible points = 1.400000 m= 29162 mr = 55306 m= 4567 mr = 20968 m= 281 mr = 2771 m= 6 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 881 time to turn everything in is 0.4100000 number of dielectric boundary points 35056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 22936 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) : 0.6010569 object centre at (A) : 8.964501 8.203499 32.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1883810E-03 -2.9250268E-02 midg,1,midg; midg,igrid,midg 3.4619197E-02 -2.9837774E-02 1,midg,midg; igrid,midg,midg -8.2330382E-04 -1.8650459E-03 gauss-seidel spectral radius is 0.9985302 estimated iterations to convergence 207 setup time was (sec) 0.6200000 now iterating at: 14:00:23 rms-change max change #iterations 4.289107 172.9607 at 10iterations 1.942227 63.29841 at 20iterations 0.8823225 27.55263 at 30iterations 0.4018364 13.10557 at 40iterations 0.1822667 5.954044 at 50iterations 8.2808271E-02 2.639145 at 60iterations 3.7716061E-02 1.155304 at 70iterations 1.7153407E-02 0.5305201 at 80iterations 7.8436946E-03 0.2298832 at 90iterations 3.5940788E-03 0.1149826 at 100iterations 1.6439843E-03 4.9912453E-02 at 110iterations 7.5621944E-04 2.2227049E-02 at 120iterations finished qdiffx linear iterations at : 14:00:30 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 7.5621944E-04 2.2227049E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 14:00:31 7.899u 0.203s 0:08.78 92.1% 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 Mon Oct 10 2011 at 14:00:31 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3065 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: 2.704756 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): -18.77500 36.70400 ymin,ymax (A): -21.41100 37.81800 zmin,zma (A): 3.935000 60.55700 x,y,z range (A): 55.47900 59.22900 56.62200 scale (grids/A): 2.704756 object centre (A): 8.964501 8.203499 32.24600 number of atom coordinates read : 3065 total number of charged atoms : 2928 net assigned charge : -2.499991 assigned positive charge : 467.0289 centred at (gu) : 83.13010 91.40291 80.96329 assigned negative charge : -469.5301 centred at (gu) : 83.07355 91.98393 81.32617 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27583 grid for indexing accessible points = 1.400000 m= 94135 mr = 133979 m= 34084 mr = 76178 m= 8224 mr = 26972 m= 1165 mr = 5987 m= 60 mr = 765 m= 0 mr = 12 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 3164 time to turn everything in is 1.040000 number of dielectric boundary points 79083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 23419 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) : 1.803171 object centre at (A) : 8.964501 8.203499 32.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0914939E-02 -0.4631517 midg,1,midg; midg,igrid,midg 0.5485471 -0.4843416 1,midg,midg; igrid,midg,midg 0.1729175 -5.5675775E-02 gauss-seidel spectral radius is 0.9992425 estimated iterations to convergence 287 setup time was (sec) 1.280000 now iterating at: 14:00:32 rms-change max change #iterations 10.34103 253.7896 at 10iterations 6.046799 142.2954 at 20iterations 3.513920 70.10243 at 30iterations 2.028031 41.37223 at 40iterations 1.168243 22.71369 at 50iterations 0.6725361 13.57978 at 60iterations 0.3854418 8.110065 at 70iterations 0.2202855 3.929756 at 80iterations 0.1264229 2.400146 at 90iterations 7.2317690E-02 1.333969 at 100iterations 4.1348103E-02 0.7483978 at 110iterations 2.3631621E-02 0.4500275 at 120iterations 1.3536873E-02 0.2754135 at 130iterations 7.7336915E-03 0.1334610 at 140iterations 4.4302600E-03 8.0879211E-02 at 150iterations 2.5399264E-03 4.4883728E-02 at 160iterations 1.4647986E-03 2.7486801E-02 at 170iterations 8.4911089E-04 1.4793396E-02 at 180iterations finished qdiffx linear iterations at : 14:00:44 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 8.4911089E-04 1.4793396E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 14:00:45 12.906u 0.209s 0:13.93 94.0% 0+0k 0+0io 0pf+0w