Sat Oct 8 11:49:19 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 11:49:19 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 = 3482 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: 0.5292028 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): -4.238000 49.53200 ymin,ymax (A): -22.36900 35.30400 zmin,zma (A): 18.79600 86.06700 x,y,z range (A): 53.77000 57.67300 67.27100 scale (grids/A): 0.5292028 object centre (A): 22.64700 6.467499 52.43150 number of atom coordinates read : 3482 total number of charged atoms : 3320 net assigned charge : -3.499992 assigned positive charge : 513.2339 centred at (gu) : 91.24590 91.69329 90.72813 assigned negative charge : -516.7357 centred at (gu) : 91.14839 91.66341 90.79912 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6270 nv = 96 ne = 84 npr = 68878 no. pairs analyzed = 68878 no. exposed pairs = 4609 no. arc points = 32553 no. surface atoms = 1556 nbur = 1926 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 261 mr = 3106 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 502 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3812798E-10 -4.8625476E-10 midg,1,midg; midg,igrid,midg -1.5416028E-10 1.0385246E-11 1,midg,midg; igrid,midg,midg -3.7290762E-10 3.7848749E-10 gauss-seidel spectral radius is 0.9816470 estimated iterations to convergence 61 setup time was (sec) 0.7500000 now iterating at: 11:49:21 rms-change max change #iterations 6.8417571E-02 12.44289 at 10iterations 4.1549066E-03 0.6133862 at 20iterations 3.0091961E-04 4.1110992E-02 at 30iterations 4.8414975E-05 8.2063675E-03 at 40iterations 1.3044004E-05 2.2583008E-03 at 50iterations finished qdiffx linear iterations at : 11:49:25 total time elapsed so far: 5.170000 # loops : 50 mean,max change (kT/e) : 1.3044004E-05 2.2583008E-03 energy calculations done at 5.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 11:49:25 5.348u 0.436s 0:06.07 95.0% 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 11:49:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3482 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: 1.587608 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): -4.238000 49.53200 ymin,ymax (A): -22.36900 35.30400 zmin,zma (A): 18.79600 86.06700 x,y,z range (A): 53.77000 57.67300 67.27100 scale (grids/A): 1.587608 object centre (A): 22.64700 6.467499 52.43150 number of atom coordinates read : 3482 total number of charged atoms : 3320 net assigned charge : -3.499992 assigned positive charge : 513.2339 centred at (gu) : 93.73679 95.07836 92.18301 assigned negative charge : -516.7357 centred at (gu) : 93.44456 94.98986 92.39674 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32553 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20372 mr = 47182 m= 1884 mr = 13301 m= 55 mr = 849 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 32004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 443 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 25203 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) : 0.5292028 object centre at (A) : 22.64700 6.467499 52.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2020749E-03 -7.5481045E-03 midg,1,midg; midg,igrid,midg 1.1323734E-04 4.0003206E-03 1,midg,midg; igrid,midg,midg -7.9865195E-03 -3.9009214E-03 gauss-seidel spectral radius is 0.9981259 estimated iterations to convergence 184 setup time was (sec) 0.9100000 now iterating at: 11:49:27 rms-change max change #iterations 3.367201 156.1776 at 10iterations 1.377851 55.47838 at 20iterations 0.5654610 22.45643 at 30iterations 0.2329125 8.307564 at 40iterations 9.5406443E-02 3.683870 at 50iterations 3.9317355E-02 1.484375 at 60iterations 1.6182814E-02 0.5848942 at 70iterations 6.6537266E-03 0.2238922 at 80iterations 2.7487816E-03 0.1023174 at 90iterations 1.1414773E-03 4.1839600E-02 at 100iterations 4.7535400E-04 1.6614914E-02 at 110iterations 2.0432510E-04 6.7787170E-03 at 120iterations finished qdiffx linear iterations at : 11:49:38 total time elapsed so far: 11.63000 # loops : 120 mean,max change (kT/e) : 2.0432510E-04 6.7787170E-03 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 11:49:38 11.810u 0.471s 0:12.59 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 11:49:38 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 = 3482 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: 2.381412 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): -4.238000 49.53200 ymin,ymax (A): -22.36900 35.30400 zmin,zma (A): 18.79600 86.06700 x,y,z range (A): 53.77000 57.67300 67.27100 scale (grids/A): 2.381412 object centre (A): 22.64700 6.467499 52.43150 number of atom coordinates read : 3482 total number of charged atoms : 3320 net assigned charge : -3.499992 assigned positive charge : 513.2339 centred at (gu) : 95.60500 97.61718 93.27425 assigned negative charge : -516.7357 centred at (gu) : 95.16682 97.48462 93.59498 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 165134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32553 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72104 mr = 116120 m= 18753 mr = 55478 m= 2794 mr = 13409 m= 178 mr = 1759 m= 0 mr = 62 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 72135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 26526 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) : 1.587608 object centre at (A) : 22.64700 6.467499 52.43150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1237513 -9.1326192E-02 midg,1,midg; midg,igrid,midg 1.0040335E-02 8.1770249E-02 1,midg,midg; igrid,midg,midg -8.4589392E-02 -9.3823217E-02 gauss-seidel spectral radius is 0.9991342 estimated iterations to convergence 268 setup time was (sec) 1.800000 now iterating at: 11:49:40 rms-change max change #iterations 8.984855 283.1858 at 10iterations 5.086524 134.0194 at 20iterations 2.856510 72.71687 at 30iterations 1.597088 40.29652 at 40iterations 0.8879705 21.38217 at 50iterations 0.4937861 11.32002 at 60iterations 0.2731682 5.669373 at 70iterations 0.1510214 3.312991 at 80iterations 8.3401650E-02 1.771067 at 90iterations 4.5999248E-02 0.9501143 at 100iterations 2.5377365E-02 0.5114193 at 110iterations 1.3989827E-02 0.2846285 at 120iterations 7.6954467E-03 0.1592350 at 130iterations 4.2359456E-03 8.5463047E-02 at 140iterations 2.3331244E-03 4.5370102E-02 at 150iterations 1.2852092E-03 2.4277687E-02 at 160iterations 7.0808770E-04 1.5524387E-02 at 170iterations 3.9198634E-04 8.2778931E-03 at 180iterations finished qdiffx linear iterations at : 11:49:59 total time elapsed so far: 20.49000 # loops : 180 mean,max change (kT/e) : 3.9198634E-04 8.2778931E-03 energy calculations done at 20.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.66000 DelPhi exited at 11:50:00 20.667u 0.480s 0:21.47 98.4% 0+0k 0+0io 0pf+0w