Sun Oct 9 16:32:43 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 Sun Oct 9 2011 at 16:32:44 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 = 2313 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: 0.5752327 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): -25.68800 27.92100 ymin,ymax (A): -16.33600 45.55200 zmin,zma (A): -25.86500 25.17100 x,y,z range (A): 53.60900 61.88800 51.03600 scale (grids/A): 0.5752327 object centre (A): 1.116500 14.60800 -0.3470001 number of atom coordinates read : 2313 total number of charged atoms : 2176 net assigned charge : 0.5000049 assigned positive charge : 336.5791 centred at (gu) : 90.82541 92.40613 90.67080 assigned negative charge : -336.0799 centred at (gu) : 90.65810 92.24375 90.68743 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5057 nv = 96 ne = 84 npr = 46183 no. pairs analyzed = 46183 no. exposed pairs = 3137 no. arc points = 22113 no. surface atoms = 1066 nbur = 1247 mkacc time = 6.9999993E-02 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= 211 mr = 2433 m= 0 mr = 3 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1178198E-10 -2.6058344E-10 midg,1,midg; midg,igrid,midg -1.3102720E-09 4.0536841E-09 1,midg,midg; igrid,midg,midg -1.9627895E-09 2.8363454E-09 gauss-seidel spectral radius is 0.9843564 estimated iterations to convergence 66 setup time was (sec) 0.3700000 now iterating at: 16:32:44 rms-change max change #iterations 7.5237639E-02 14.09853 at 10iterations 5.7114009E-03 0.9897633 at 20iterations 4.4732983E-04 7.2990417E-02 at 30iterations 3.3594144E-05 7.3642731E-03 at 40iterations 3.0123881E-06 5.1879883E-04 at 50iterations finished qdiffx linear iterations at : 16:32:47 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.0123881E-06 5.1879883E-04 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 16:32:47 3.412u 0.194s 0:03.90 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 Sun Oct 9 2011 at 16:32:47 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 = 2313 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.725698 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): -25.68800 27.92100 ymin,ymax (A): -16.33600 45.55200 zmin,zma (A): -25.86500 25.17100 x,y,z range (A): 53.60900 61.88800 51.03600 scale (grids/A): 1.725698 object centre (A): 1.116500 14.60800 -0.3470001 number of atom coordinates read : 2313 total number of charged atoms : 2176 net assigned charge : 0.5000049 assigned positive charge : 336.5791 centred at (gu) : 92.47569 97.21793 92.01223 assigned negative charge : -336.0799 centred at (gu) : 91.97425 96.73125 92.06229 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 55620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22113 grid for indexing accessible points = 1.400000 m= 16615 mr = 35946 m= 1918 mr = 11038 m= 59 mr = 982 m= 0 mr = 6 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 292 time to turn everything in is 0.2700000 number of dielectric boundary points 26240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 16875 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) : 0.5752327 object centre at (A) : 1.116500 14.60800 -0.3470001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4973966E-03 -5.1638414E-03 midg,1,midg; midg,igrid,midg -5.4395059E-03 -1.9102152E-02 1,midg,midg; igrid,midg,midg -5.6791161E-03 2.1568101E-02 gauss-seidel spectral radius is 0.9983152 estimated iterations to convergence 193 setup time was (sec) 0.4800000 now iterating at: 16:32:48 rms-change max change #iterations 3.180965 164.7909 at 10iterations 1.356224 50.76306 at 20iterations 0.5822672 22.21893 at 30iterations 0.2499496 10.52076 at 40iterations 0.1077593 4.177334 at 50iterations 4.6351723E-02 1.813519 at 60iterations 1.9871725E-02 0.7564683 at 70iterations 8.5418550E-03 0.3301485 at 80iterations 3.6693425E-03 0.1454358 at 90iterations 1.5794093E-03 6.2336445E-02 at 100iterations 6.7998300E-04 2.5068760E-02 at 110iterations 2.9341513E-04 1.0916531E-02 at 120iterations finished qdiffx linear iterations at : 16:32:55 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 2.9341513E-04 1.0916531E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 16:32:56 7.735u 0.236s 0:08.30 95.9% 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 Sun Oct 9 2011 at 16:32:56 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 = 2313 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.588547 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): -25.68800 27.92100 ymin,ymax (A): -16.33600 45.55200 zmin,zma (A): -25.86500 25.17100 x,y,z range (A): 53.60900 61.88800 51.03600 scale (grids/A): 2.588547 object centre (A): 1.116500 14.60800 -0.3470001 number of atom coordinates read : 2313 total number of charged atoms : 2176 net assigned charge : 0.5000049 assigned positive charge : 336.5791 centred at (gu) : 93.71346 100.8266 93.01821 assigned negative charge : -336.0799 centred at (gu) : 92.96141 100.0967 93.09341 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 129066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22113 grid for indexing accessible points = 1.400000 m= 56581 mr = 88463 m= 16717 mr = 43371 m= 3077 mr = 12480 m= 266 mr = 2112 m= 9 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 931 time to turn everything in is 0.6900000 number of dielectric boundary points 59143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17397 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) : 1.725698 object centre at (A) : 1.116500 14.60800 -0.3470001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1027319 -4.8545156E-02 midg,1,midg; midg,igrid,midg -5.9722885E-02 -0.5638142 1,midg,midg; igrid,midg,midg -7.1908079E-02 0.2915595 gauss-seidel spectral radius is 0.9991694 estimated iterations to convergence 274 setup time was (sec) 0.9300000 now iterating at: 16:32:57 rms-change max change #iterations 8.025353 275.7700 at 10iterations 4.550992 137.1471 at 20iterations 2.577370 62.64133 at 30iterations 1.448423 38.34767 at 40iterations 0.8147133 21.38322 at 50iterations 0.4563071 10.68571 at 60iterations 0.2552207 6.209193 at 70iterations 0.1422058 3.126705 at 80iterations 7.9302877E-02 1.899427 at 90iterations 4.4184156E-02 1.011154 at 100iterations 2.4615103E-02 0.5050049 at 110iterations 1.3680983E-02 0.3592319 at 120iterations 7.6141902E-03 0.1671518 at 130iterations 4.2321631E-03 9.4022512E-02 at 140iterations 2.3519422E-03 5.2818298E-02 at 150iterations 1.3082792E-03 3.2033920E-02 at 160iterations 7.2825066E-04 1.8199921E-02 at 170iterations 4.0397554E-04 9.5024109E-03 at 180iterations finished qdiffx linear iterations at : 16:33:08 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 4.0397554E-04 9.5024109E-03 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 16:33:09 12.191u 0.207s 0:12.71 97.4% 0+0k 0+0io 0pf+0w