Mon Oct 10 10:29:33 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 10:29:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2784 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: 0.5530441 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): -22.59300 41.77800 ymin,ymax (A): -12.30600 43.29100 zmin,zma (A): -1.877000 52.34500 x,y,z range (A): 64.37100 55.59700 54.22200 scale (grids/A): 0.5530441 object centre (A): 9.592500 15.49250 25.23400 number of atom coordinates read : 2784 total number of charged atoms : 2636 net assigned charge : 10.00002 assigned positive charge : 406.6281 centred at (gu) : 91.94946 91.54150 86.78957 assigned negative charge : -396.6285 centred at (gu) : 92.02981 91.61629 86.57800 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5653 nv = 96 ne = 84 npr = 54076 no. pairs analyzed = 54076 no. exposed pairs = 4155 no. arc points = 30201 no. surface atoms = 1385 nbur = 1399 mkacc time = 0.1400000 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 = 1.540000 m= 240 mr = 2441 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7321 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7610360E-09 1.1252076E-09 midg,1,midg; midg,igrid,midg 9.9495490E-10 4.4517587E-10 1,midg,midg; igrid,midg,midg 9.2855634E-10 4.1791939E-10 gauss-seidel spectral radius is 0.9831387 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 10:29:34 rms-change max change #iterations 7.1681708E-02 14.88473 at 10iterations 4.7562239E-03 0.9704285 at 20iterations 3.5742280E-04 6.3514709E-02 at 30iterations 3.5280551E-05 6.1588287E-03 at 40iterations 5.9570998E-06 9.7346306E-04 at 50iterations finished qdiffx linear iterations at : 10:29:38 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 5.9570998E-06 9.7346306E-04 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 10:29:38 4.583u 0.377s 0:05.24 94.4% 0+0k 0+0io 6pf+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 10:29:38 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 = 2784 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: 1.659132 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): -22.59300 41.77800 ymin,ymax (A): -12.30600 43.29100 zmin,zma (A): -1.877000 52.34500 x,y,z range (A): 64.37100 55.59700 54.22200 scale (grids/A): 1.659132 object centre (A): 9.592500 15.49250 25.23400 number of atom coordinates read : 2784 total number of charged atoms : 2636 net assigned charge : 10.00002 assigned positive charge : 406.6281 centred at (gu) : 95.84790 94.62432 80.36826 assigned negative charge : -396.6285 centred at (gu) : 96.08909 94.84856 79.73392 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30201 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18246 mr = 37602 m= 1835 mr = 11372 m= 43 mr = 645 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 32116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20310 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) : 0.5530441 object centre at (A) : 9.592500 15.49250 25.23400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5363029E-04 9.3274927E-03 midg,1,midg; midg,igrid,midg 1.6311988E-02 1.7692870E-02 1,midg,midg; igrid,midg,midg -9.7721359E-03 -1.5315739E-02 gauss-seidel spectral radius is 0.9982318 estimated iterations to convergence 189 setup time was (sec) 0.8200000 now iterating at: 10:29:39 rms-change max change #iterations 3.250656 174.8091 at 10iterations 1.364046 54.14421 at 20iterations 0.5674506 22.60012 at 30iterations 0.2388420 10.66140 at 40iterations 9.9997558E-02 3.533779 at 50iterations 4.2009238E-02 1.681009 at 60iterations 1.7759692E-02 0.6526270 at 70iterations 7.4317185E-03 0.2768669 at 80iterations 3.1296045E-03 0.1107368 at 90iterations 1.3149255E-03 4.8684120E-02 at 100iterations 5.5521476E-04 2.1841049E-02 at 110iterations 2.3374398E-04 8.5434914E-03 at 120iterations finished qdiffx linear iterations at : 10:29:49 total time elapsed so far: 10.82000 # loops : 120 mean,max change (kT/e) : 2.3374398E-04 8.5434914E-03 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 10:29:50 10.980u 0.457s 0:11.69 97.7% 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 10:29:50 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 = 2784 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: 2.488698 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): -22.59300 41.77800 ymin,ymax (A): -12.30600 43.29100 zmin,zma (A): -1.877000 52.34500 x,y,z range (A): 64.37100 55.59700 54.22200 scale (grids/A): 2.488698 object centre (A): 9.592500 15.49250 25.23400 number of atom coordinates read : 2784 total number of charged atoms : 2636 net assigned charge : 10.00002 assigned positive charge : 406.6281 centred at (gu) : 98.77178 96.93629 75.55231 assigned negative charge : -396.6285 centred at (gu) : 99.13361 97.27274 74.60075 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 142632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30201 grid for indexing accessible points = 1.400000 m= 61848 mr = 92954 m= 17354 mr = 45740 m= 2597 mr = 12003 m= 153 mr = 1333 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 72509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 21065 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) : 1.659132 object centre at (A) : 9.592500 15.49250 25.23400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2192729E-02 0.1133558 midg,1,midg; midg,igrid,midg 0.2880699 0.2342849 1,midg,midg; igrid,midg,midg -0.3159737 -0.4066564 gauss-seidel spectral radius is 0.9991522 estimated iterations to convergence 271 setup time was (sec) 1.600000 now iterating at: 10:29:52 rms-change max change #iterations 8.618855 272.5644 at 10iterations 4.982111 164.5009 at 20iterations 2.852433 81.85182 at 30iterations 1.609651 45.14030 at 40iterations 0.9067674 24.07943 at 50iterations 0.5094810 11.96995 at 60iterations 0.2842129 7.376823 at 70iterations 0.1582342 3.536091 at 80iterations 8.8213466E-02 2.199596 at 90iterations 4.8963141E-02 1.332749 at 100iterations 2.7205704E-02 0.7673187 at 110iterations 1.5054269E-02 0.3394284 at 120iterations 8.3516054E-03 0.1998892 at 130iterations 4.6212715E-03 0.1017494 at 140iterations 2.5500834E-03 7.1792603E-02 at 150iterations 1.4105759E-03 3.1641006E-02 at 160iterations 7.8011956E-04 1.7326355E-02 at 170iterations 4.3089670E-04 9.7389221E-03 at 180iterations finished qdiffx linear iterations at : 10:30:07 total time elapsed so far: 17.20000 # loops : 180 mean,max change (kT/e) : 4.3089670E-04 9.7389221E-03 energy calculations done at 17.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.36000 DelPhi exited at 10:30:08 17.368u 0.453s 0:18.13 98.2% 0+0k 0+0io 0pf+0w