Tue Oct 11 06:32:36 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 Tue Oct 11 2011 at 06:32:36 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 = 2072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7246230 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): -40.97800 -1.171000 ymin,ymax (A): -26.98100 18.72200 zmin,zma (A): -15.02400 34.10500 x,y,z range (A): 39.80700 45.70300 49.12900 scale (grids/A): 0.7246230 object centre (A): -21.07450 -4.129499 9.540500 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 315.5060 centred at (gu) : 91.30704 89.68957 89.18656 assigned negative charge : -309.0062 centred at (gu) : 91.34560 89.81383 89.13866 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7474 nv = 96 ne = 84 npr = 41374 no. pairs analyzed = 41374 no. exposed pairs = 2480 no. arc points = 17035 no. surface atoms = 845 nbur = 1227 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 4328 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1537 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5002278E-08 9.9454176E-08 midg,1,midg; midg,igrid,midg 1.7935103E-07 -6.7789192E-09 1,midg,midg; igrid,midg,midg 8.5682515E-08 6.8679839E-08 gauss-seidel spectral radius is 0.9900680 estimated iterations to convergence 82 setup time was (sec) 0.3600000 now iterating at: 06:32:36 rms-change max change #iterations 0.2245031 31.44329 at 10iterations 2.9157793E-02 3.988174 at 20iterations 3.8201369E-03 0.4740410 at 30iterations 5.9385994E-04 7.5955391E-02 at 40iterations 1.2379604E-04 1.6132355E-02 at 50iterations finished qdiffx linear iterations at : 06:32:39 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.2379604E-04 1.6132355E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:32:39 3.315u 0.183s 0:03.78 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 Tue Oct 11 2011 at 06:32:40 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 = 2072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.173869 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): -40.97800 -1.171000 ymin,ymax (A): -26.98100 18.72200 zmin,zma (A): -15.02400 34.10500 x,y,z range (A): 39.80700 45.70300 49.12900 scale (grids/A): 2.173869 object centre (A): -21.07450 -4.129499 9.540500 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 315.5060 centred at (gu) : 93.92120 89.06863 87.55962 assigned negative charge : -309.0062 centred at (gu) : 94.03691 89.44170 87.41597 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 32196 mr = 56306 m= 6548 mr = 24696 m= 632 mr = 4452 m= 17 mr = 337 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 32414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15468 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) : 0.7246230 object centre at (A) : -21.07450 -4.129499 9.540500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1798346E-02 3.9064616E-02 midg,1,midg; midg,igrid,midg 5.9450939E-02 2.0126730E-02 1,midg,midg; igrid,midg,midg 1.4864189E-02 3.8939133E-02 gauss-seidel spectral radius is 0.9988777 estimated iterations to convergence 236 setup time was (sec) 0.6200000 now iterating at: 06:32:40 rms-change max change #iterations 4.805131 197.6443 at 10iterations 2.412767 98.99274 at 20iterations 1.224060 37.21002 at 30iterations 0.6157289 18.36654 at 40iterations 0.3098311 10.33713 at 50iterations 0.1564427 4.473144 at 60iterations 7.8818351E-02 2.202196 at 70iterations 3.9779443E-02 1.117506 at 80iterations 2.0070689E-02 0.5666161 at 90iterations 1.0159533E-02 0.3684397 at 100iterations 5.1438953E-03 0.1460981 at 110iterations 2.6135191E-03 7.6958656E-02 at 120iterations finished qdiffx linear iterations at : 06:32:47 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 2.6135191E-03 7.6958656E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 06:32:48 7.801u 0.191s 0:08.47 94.3% 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 Tue Oct 11 2011 at 06:32:48 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 = 2072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.260803 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): -40.97800 -1.171000 ymin,ymax (A): -26.98100 18.72200 zmin,zma (A): -15.02400 34.10500 x,y,z range (A): 39.80700 45.70300 49.12900 scale (grids/A): 3.260803 object centre (A): -21.07450 -4.129499 9.540500 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 315.5060 centred at (gu) : 95.88173 88.60297 86.33940 assigned negative charge : -309.0062 centred at (gu) : 96.05551 89.16252 86.12407 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 181655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 99988 mr = 135504 m= 41628 mr = 83628 m= 12407 mr = 34532 m= 2539 mr = 9696 m= 314 mr = 1874 m= 17 mr = 237 m= 0 mr = 2 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 73075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15552 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) : 2.173869 object centre at (A) : -21.07450 -4.129499 9.540500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3313451 0.2325883 midg,1,midg; midg,igrid,midg 0.4777059 0.1880708 1,midg,midg; igrid,midg,midg 7.9179659E-02 0.4319602 gauss-seidel spectral radius is 0.9993090 estimated iterations to convergence 300 setup time was (sec) 1.460000 now iterating at: 06:32:50 rms-change max change #iterations 10.52820 439.2722 at 10iterations 6.252733 149.6091 at 20iterations 3.713415 89.46036 at 30iterations 2.201374 49.60994 at 40iterations 1.304978 23.88947 at 50iterations 0.7700188 15.52446 at 60iterations 0.4542086 8.735508 at 70iterations 0.2681631 5.540909 at 80iterations 0.1579575 2.632065 at 90iterations 9.3111135E-02 1.547047 at 100iterations 5.4978866E-02 1.031165 at 110iterations 3.2573715E-02 0.5482788 at 120iterations 1.9362630E-02 0.3604889 at 130iterations 1.1633253E-02 0.1953030 at 140iterations 7.1652206E-03 0.1256466 at 150iterations 4.5616506E-03 7.9875946E-02 at 160iterations 3.0399165E-03 5.7868958E-02 at 170iterations 2.1555722E-03 3.8982391E-02 at 180iterations finished qdiffx linear iterations at : 06:33:01 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 2.1555722E-03 3.8982391E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 06:33:01 12.962u 0.211s 0:13.45 97.9% 0+0k 0+0io 0pf+0w