Mon Oct 10 14:05:46 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 14:05:46 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 = 2328 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: 0.6677170 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): -11.98200 33.04700 ymin,ymax (A): -22.12400 29.91900 zmin,zma (A): -10.74300 42.57300 x,y,z range (A): 45.02900 52.04300 53.31600 scale (grids/A): 0.6677170 object centre (A): 10.53250 3.897499 15.91500 number of atom coordinates read : 2328 total number of charged atoms : 2188 net assigned charge : 3.500003 assigned positive charge : 345.2904 centred at (gu) : 91.58644 90.79649 90.15576 assigned negative charge : -341.7907 centred at (gu) : 91.50648 90.76466 89.92336 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 45413 no. pairs analyzed = 45413 no. exposed pairs = 3006 no. arc points = 21400 no. surface atoms = 1024 nbur = 1304 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3859 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3000000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2042 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8223 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8493418E-08 6.0377261E-08 midg,1,midg; midg,igrid,midg 3.2874188E-09 2.0266745E-08 1,midg,midg; igrid,midg,midg -4.5294688E-09 3.7915168E-08 gauss-seidel spectral radius is 0.9883571 estimated iterations to convergence 76 setup time was (sec) 0.5500000 now iterating at: 14:05:46 rms-change max change #iterations 0.1601800 23.09905 at 10iterations 1.7350441E-02 2.337483 at 20iterations 1.9295474E-03 0.2951965 at 30iterations 2.7060995E-04 3.8524628E-02 at 40iterations 8.0198362E-05 1.4457703E-02 at 50iterations finished qdiffx linear iterations at : 14:05:49 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 8.0198362E-05 1.4457703E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:05:50 3.535u 0.248s 0:04.23 89.1% 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 14:05:50 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 = 2328 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.003151 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): -11.98200 33.04700 ymin,ymax (A): -22.12400 29.91900 zmin,zma (A): -10.74300 42.57300 x,y,z range (A): 45.02900 52.04300 53.31600 scale (grids/A): 2.003151 object centre (A): 10.53250 3.897499 15.91500 number of atom coordinates read : 2328 total number of charged atoms : 2188 net assigned charge : 3.500003 assigned positive charge : 345.2904 centred at (gu) : 94.75905 92.38918 90.46691 assigned negative charge : -341.7907 centred at (gu) : 94.51922 92.29384 89.76982 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21400 grid for indexing accessible points = 1.400000 m= 27972 mr = 53041 m= 4570 mr = 20287 m= 325 mr = 2810 m= 4 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.5800000 number of dielectric boundary points 34084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17324 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) : 0.6677170 object centre at (A) : 10.53250 3.897499 15.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1328532E-02 5.8259480E-03 midg,1,midg; midg,igrid,midg 3.8256738E-02 2.9140588E-02 1,midg,midg; igrid,midg,midg -1.5517151E-02 1.0264190E-02 gauss-seidel spectral radius is 0.9987423 estimated iterations to convergence 223 setup time was (sec) 0.9000000 now iterating at: 14:05:51 rms-change max change #iterations 4.345917 174.2580 at 10iterations 2.094106 76.51547 at 20iterations 1.013110 30.53926 at 30iterations 0.4888937 15.58044 at 40iterations 0.2361958 8.090164 at 50iterations 0.1139611 3.386122 at 60iterations 5.5358075E-02 1.828398 at 70iterations 2.6746897E-02 0.8605289 at 80iterations 1.2931188E-02 0.4906693 at 90iterations 6.2602218E-03 0.1951323 at 100iterations 3.0297586E-03 9.3262672E-02 at 110iterations 1.4686491E-03 4.0271759E-02 at 120iterations finished qdiffx linear iterations at : 14:05:58 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.4686491E-03 4.0271759E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 14:05:59 8.125u 0.262s 0:08.83 94.9% 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 14:05:59 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 = 2328 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.004726 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): -11.98200 33.04700 ymin,ymax (A): -22.12400 29.91900 zmin,zma (A): -10.74300 42.57300 x,y,z range (A): 45.02900 52.04300 53.31600 scale (grids/A): 3.004726 object centre (A): 10.53250 3.897499 15.91500 number of atom coordinates read : 2328 total number of charged atoms : 2188 net assigned charge : 3.500003 assigned positive charge : 345.2904 centred at (gu) : 97.13825 93.58371 90.70033 assigned negative charge : -341.7907 centred at (gu) : 96.77878 93.44075 89.65479 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 179245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21400 grid for indexing accessible points = 1.400000 m= 90360 mr = 128660 m= 32953 mr = 73471 m= 8310 mr = 26157 m= 1469 mr = 6130 m= 149 mr = 1073 m= 2 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 303 time to turn everything in is 1.520000 number of dielectric boundary points 76891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 17504 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) : 2.003151 object centre at (A) : 10.53250 3.897499 15.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3500831 -9.6014500E-02 midg,1,midg; midg,igrid,midg 0.5387371 0.1072263 1,midg,midg; igrid,midg,midg -0.2289392 0.1030452 gauss-seidel spectral radius is 0.9992900 estimated iterations to convergence 296 setup time was (sec) 1.860000 now iterating at: 14:06:01 rms-change max change #iterations 10.08347 455.0118 at 10iterations 5.954205 158.8880 at 20iterations 3.513924 67.79111 at 30iterations 2.058252 41.90485 at 40iterations 1.210795 23.52753 at 50iterations 0.7099514 13.55534 at 60iterations 0.4153103 8.122315 at 70iterations 0.2421678 4.463062 at 80iterations 0.1413232 2.466790 at 90iterations 8.2529321E-02 1.583567 at 100iterations 4.8131946E-02 0.9171166 at 110iterations 2.8005695E-02 0.4832120 at 120iterations 1.6300268E-02 0.3085861 at 130iterations 9.4961142E-03 0.1615181 at 140iterations 5.5293627E-03 9.5520020E-02 at 150iterations 3.2174159E-03 5.8142662E-02 at 160iterations 1.8748225E-03 3.4398079E-02 at 170iterations 1.0906853E-03 1.8626213E-02 at 180iterations finished qdiffx linear iterations at : 14:06:12 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 1.0906853E-03 1.8626213E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 14:06:13 13.364u 0.243s 0:14.28 95.2% 0+0k 0+0io 0pf+0w