Tue Oct 11 08:35:26 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 Tue Oct 11 2011 at 08:35:26 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 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: 0.6725864 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): -10.85100 36.64600 ymin,ymax (A): 6.707000 55.66100 zmin,zma (A): -7.421000 45.50900 x,y,z range (A): 47.49700 48.95400 52.93000 scale (grids/A): 0.6725864 object centre (A): 12.89750 31.18400 19.04400 number of atom coordinates read : 2701 total number of charged atoms : 2548 net assigned charge : 5.500013 assigned positive charge : 410.1239 centred at (gu) : 90.05022 90.49036 91.27031 assigned negative charge : -404.6244 centred at (gu) : 89.80409 90.32729 91.31928 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 55242 no. pairs analyzed = 55242 no. exposed pairs = 3318 no. arc points = 23177 no. surface atoms = 1118 nbur = 1583 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4682 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 3951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2127 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5829442E-08 6.9716499E-09 midg,1,midg; midg,igrid,midg -2.4578817E-08 7.1746427E-08 1,midg,midg; igrid,midg,midg -5.1288232E-08 8.8263846E-08 gauss-seidel spectral radius is 0.9885476 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 08:35:27 rms-change max change #iterations 0.1864605 24.95994 at 10iterations 2.1205721E-02 2.929583 at 20iterations 2.4634774E-03 0.3126259 at 30iterations 3.3706013E-04 4.8713684E-02 at 40iterations 6.9263966E-05 8.3980560E-03 at 50iterations finished qdiffx linear iterations at : 08:35:29 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 6.9263966E-05 8.3980560E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 08:35:30 3.057u 0.140s 0:03.73 85.5% 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 08:35:30 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 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: 2.017759 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): -10.85100 36.64600 ymin,ymax (A): 6.707000 55.66100 zmin,zma (A): -7.421000 45.50900 x,y,z range (A): 47.49700 48.95400 52.93000 scale (grids/A): 2.017759 object centre (A): 12.89750 31.18400 19.04400 number of atom coordinates read : 2701 total number of charged atoms : 2548 net assigned charge : 5.500013 assigned positive charge : 410.1239 centred at (gu) : 90.15002 91.47072 93.81034 assigned negative charge : -404.6244 centred at (gu) : 89.41220 90.98167 93.95766 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23177 grid for indexing accessible points = 1.400000 m= 34533 mr = 61980 m= 6464 mr = 26237 m= 511 mr = 4359 m= 6 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 262 time to turn everything in is 0.6000000 number of dielectric boundary points 36387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20152 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) : 0.6725864 object centre at (A) : 12.89750 31.18400 19.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4765730E-02 9.0089161E-03 midg,1,midg; midg,igrid,midg -1.2697467E-02 4.3367110E-02 1,midg,midg; igrid,midg,midg -1.5877537E-02 7.5167097E-02 gauss-seidel spectral radius is 0.9987868 estimated iterations to convergence 227 setup time was (sec) 0.8700000 now iterating at: 08:35:31 rms-change max change #iterations 4.918856 204.2687 at 10iterations 2.414453 75.71088 at 20iterations 1.180261 36.76382 at 30iterations 0.5779201 16.94604 at 40iterations 0.2841552 8.120217 at 50iterations 0.1395064 3.722511 at 60iterations 6.8456732E-02 2.022537 at 70iterations 3.3407547E-02 0.9916129 at 80iterations 1.6410334E-02 0.4702435 at 90iterations 8.0452021E-03 0.2258835 at 100iterations 3.9533977E-03 0.1168098 at 110iterations 1.9487650E-03 5.7727814E-02 at 120iterations finished qdiffx linear iterations at : 08:35:37 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.9487650E-03 5.7727814E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 08:35:38 7.754u 0.157s 0:08.53 92.6% 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 08:35:38 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 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: 3.026639 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): -10.85100 36.64600 ymin,ymax (A): 6.707000 55.66100 zmin,zma (A): -7.421000 45.50900 x,y,z range (A): 47.49700 48.95400 52.93000 scale (grids/A): 3.026639 object centre (A): 12.89750 31.18400 19.04400 number of atom coordinates read : 2701 total number of charged atoms : 2548 net assigned charge : 5.500013 assigned positive charge : 410.1239 centred at (gu) : 90.22504 92.20597 95.71542 assigned negative charge : -404.6244 centred at (gu) : 89.11814 91.47252 95.93644 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 202051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23177 grid for indexing accessible points = 1.400000 m= 108468 mr = 149334 m= 43555 mr = 89991 m= 11826 mr = 35900 m= 2220 mr = 9207 m= 163 mr = 1675 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 903 time to turn everything in is 1.540000 number of dielectric boundary points 82126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 20384 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) : 2.017759 object centre at (A) : 12.89750 31.18400 19.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1164985 0.3258999 midg,1,midg; midg,igrid,midg -0.1567021 0.4595256 1,midg,midg; igrid,midg,midg -0.1357792 0.5737047 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 1.820000 now iterating at: 08:35:40 rms-change max change #iterations 11.12781 364.1158 at 10iterations 6.557998 150.6568 at 20iterations 3.857438 71.87937 at 30iterations 2.270175 39.30794 at 40iterations 1.333566 23.22381 at 50iterations 0.7808141 12.79640 at 60iterations 0.4571521 7.478939 at 70iterations 0.2675402 4.329987 at 80iterations 0.1562529 2.548769 at 90iterations 9.1378815E-02 1.613304 at 100iterations 5.3501379E-02 0.9944439 at 110iterations 3.1231262E-02 0.4971235 at 120iterations 1.8288437E-02 0.3235950 at 130iterations 1.0723697E-02 0.1687965 at 140iterations 6.3006822E-03 0.1236343 at 150iterations 3.7355998E-03 6.1836243E-02 at 160iterations 2.2399849E-03 4.0901184E-02 at 170iterations 1.3626642E-03 2.5154114E-02 at 180iterations finished qdiffx linear iterations at : 08:35:50 total time elapsed so far: 11.23000 # loops : 180 mean,max change (kT/e) : 1.3626642E-03 2.5154114E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 08:35:50 11.409u 0.172s 0:11.98 96.5% 0+0k 0+0io 0pf+0w