Sun Oct 9 00:27:49 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 00:27:49 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.5721541 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): -24.56000 37.66100 ymin,ymax (A): 20.23600 80.25900 zmin,zma (A): -29.82500 28.82600 x,y,z range (A): 62.22100 60.02299 58.65100 scale (grids/A): 0.5721541 object centre (A): 6.550502 50.24750 -0.4994993 number of atom coordinates read : 3383 total number of charged atoms : 3238 net assigned charge : 11.51404 assigned positive charge : 503.2085 centred at (gu) : 91.99640 89.17456 88.80343 assigned negative charge : -491.6962 centred at (gu) : 92.02837 88.99265 88.72433 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7592 nv = 96 ne = 84 npr = 65049 no. pairs analyzed = 65049 no. exposed pairs = 4698 no. arc points = 33413 no. surface atoms = 1562 nbur = 1821 mkacc time = 0.1200000 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 = 1.484000 m= 343 mr = 3750 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3294 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0729988E-10 2.5850373E-09 midg,1,midg; midg,igrid,midg -1.8412813E-09 4.3342534E-09 1,midg,midg; igrid,midg,midg 1.6138424E-09 2.1537276E-09 gauss-seidel spectral radius is 0.9842851 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 00:27:50 rms-change max change #iterations 9.7815447E-02 16.62870 at 10iterations 7.4976492E-03 1.157154 at 20iterations 7.9662324E-04 0.1257133 at 30iterations 2.0377642E-04 4.3466568E-02 at 40iterations 7.1875518E-05 1.5415192E-02 at 50iterations finished qdiffx linear iterations at : 00:27:53 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 7.1875518E-05 1.5415192E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 00:27:53 3.418u 0.173s 0:03.89 92.0% 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 Sun Oct 9 2011 at 00:27:53 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.716462 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): -24.56000 37.66100 ymin,ymax (A): 20.23600 80.25900 zmin,zma (A): -29.82500 28.82600 x,y,z range (A): 62.22100 60.02299 58.65100 scale (grids/A): 1.716462 object centre (A): 6.550502 50.24750 -0.4994993 number of atom coordinates read : 3383 total number of charged atoms : 3238 net assigned charge : 11.51404 assigned positive charge : 503.2085 centred at (gu) : 95.98804 87.52273 86.40920 assigned negative charge : -491.6962 centred at (gu) : 96.08480 86.97762 86.17302 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33413 grid for indexing accessible points = 1.400000 m= 27304 mr = 54899 m= 3250 mr = 18596 m= 136 mr = 1578 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 0.4000000 number of dielectric boundary points 38619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 25116 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) : 0.5721541 object centre at (A) : 6.550502 50.24750 -0.4994993 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3766661E-02 3.7924357E-02 midg,1,midg; midg,igrid,midg -1.9888597E-02 1.5838398E-02 1,midg,midg; igrid,midg,midg 6.8123960E-03 1.4259234E-02 gauss-seidel spectral radius is 0.9984200 estimated iterations to convergence 200 setup time was (sec) 0.6200000 now iterating at: 00:27:54 rms-change max change #iterations 3.954478 174.9572 at 10iterations 1.733688 64.09760 at 20iterations 0.7631792 25.37346 at 30iterations 0.3362265 10.44437 at 40iterations 0.1491184 4.748936 at 50iterations 6.5689996E-02 2.208935 at 60iterations 2.9032908E-02 0.9825783 at 70iterations 1.2927782E-02 0.4316540 at 80iterations 5.7941223E-03 0.1785707 at 90iterations 2.6422301E-03 8.5121155E-02 at 100iterations 1.2521555E-03 5.1184416E-02 at 110iterations 6.4084097E-04 2.2777557E-02 at 120iterations finished qdiffx linear iterations at : 00:28:01 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 6.4084097E-04 2.2777557E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 00:28:02 7.859u 0.205s 0:08.35 96.4% 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 Sun Oct 9 2011 at 00:28:02 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.574693 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): -24.56000 37.66100 ymin,ymax (A): 20.23600 80.25900 zmin,zma (A): -29.82500 28.82600 x,y,z range (A): 62.22100 60.02299 58.65100 scale (grids/A): 2.574693 object centre (A): 6.550502 50.24750 -0.4994993 number of atom coordinates read : 3383 total number of charged atoms : 3238 net assigned charge : 11.51404 assigned positive charge : 503.2085 centred at (gu) : 98.98170 86.28384 84.61351 assigned negative charge : -491.6962 centred at (gu) : 99.12724 85.46640 84.25939 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 192481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33413 grid for indexing accessible points = 1.400000 m= 91641 mr = 134633 m= 28438 mr = 71560 m= 5204 mr = 21376 m= 480 mr = 3271 m= 13 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 960 time to turn everything in is 1.000000 number of dielectric boundary points 87194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 25892 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) : 1.716462 object centre at (A) : 6.550502 50.24750 -0.4994993 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3631957 0.5801489 midg,1,midg; midg,igrid,midg -0.1747722 0.2011469 1,midg,midg; igrid,midg,midg 8.7227477E-03 0.1200971 gauss-seidel spectral radius is 0.9992253 estimated iterations to convergence 284 setup time was (sec) 1.230000 now iterating at: 00:28:03 rms-change max change #iterations 10.08423 252.7929 at 10iterations 5.917361 126.6316 at 20iterations 3.434120 88.44482 at 30iterations 1.986237 47.06408 at 40iterations 1.140795 23.00556 at 50iterations 0.6534399 12.20670 at 60iterations 0.3734717 7.292761 at 70iterations 0.2135711 3.972696 at 80iterations 0.1214565 2.416420 at 90iterations 6.9323182E-02 1.170545 at 100iterations 3.9478529E-02 0.7300549 at 110iterations 2.2461444E-02 0.4044189 at 120iterations 1.2781046E-02 0.2284966 at 130iterations 7.3235352E-03 0.1530075 at 140iterations 4.2136293E-03 7.6965332E-02 at 150iterations 2.4383273E-03 4.6844482E-02 at 160iterations 1.4464899E-03 2.8422356E-02 at 170iterations 8.8744116E-04 2.1856308E-02 at 180iterations finished qdiffx linear iterations at : 00:28:15 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 8.8744116E-04 2.1856308E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 00:28:15 12.939u 0.225s 0:13.47 97.6% 0+0k 0+0io 0pf+0w