Sat Oct 15 14:34:00 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 Sat Oct 15 2011 at 14:34:00 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2830 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6163434 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): -9.115000 48.64500 ymin,ymax (A): -8.374001 38.66200 zmin,zma (A): 0.4230000 54.90100 x,y,z range (A): 57.76000 47.03600 54.47800 scale (grids/A): 0.6163434 object centre (A): 19.76500 15.14400 27.66200 number of atom coordinates read : 2830 total number of charged atoms : 2689 net assigned charge : -1.985968 assigned positive charge : 428.4651 centred at (gu) : 89.26781 89.71966 88.96823 assigned negative charge : -430.4522 centred at (gu) : 89.19019 89.63150 88.93336 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7292 nv = 96 ne = 84 npr = 55748 no. pairs analyzed = 55748 no. exposed pairs = 3751 no. arc points = 26661 no. surface atoms = 1266 nbur = 1564 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3790 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2200000 number of dielectric boundary points 3810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2659 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8890 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5928825E-09 7.5018369E-10 midg,1,midg; midg,igrid,midg -7.6933153E-09 4.1635078E-09 1,midg,midg; igrid,midg,midg -7.6778397E-09 3.1755918E-09 gauss-seidel spectral radius is 0.9863979 estimated iterations to convergence 70 setup time was (sec) 0.4300000 now iterating at: 14:34:01 rms-change max change #iterations 0.1255572 18.19786 at 10iterations 1.1693062E-02 1.646507 at 20iterations 1.0495447E-03 0.1599045 at 30iterations 1.0078507E-04 1.3977051E-02 at 40iterations 1.1778250E-05 2.0079613E-03 at 50iterations finished qdiffx linear iterations at : 14:34:06 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 1.1778250E-05 2.0079613E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 14:34:07 3.827u 0.219s 0:07.39 54.5% 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 Sat Oct 15 2011 at 14:34:07 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2830 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.849030 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): -9.115000 48.64500 ymin,ymax (A): -8.374001 38.66200 zmin,zma (A): 0.4230000 54.90100 x,y,z range (A): 57.76000 47.03600 54.47800 scale (grids/A): 1.849030 object centre (A): 19.76500 15.14400 27.66200 number of atom coordinates read : 2830 total number of charged atoms : 2689 net assigned charge : -1.985968 assigned positive charge : 428.4651 centred at (gu) : 87.80271 89.15814 86.90368 assigned negative charge : -430.4522 centred at (gu) : 87.57004 88.89407 86.79952 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26661 grid for indexing accessible points = 1.400000 m= 26560 mr = 53257 m= 3691 mr = 18741 m= 184 mr = 2121 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 853 time to turn everything in is 0.4200000 number of dielectric boundary points 35325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21094 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) : 0.6163434 object centre at (A) : 19.76500 15.14400 27.66200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7347585E-03 3.3080010E-03 midg,1,midg; midg,igrid,midg -1.7048350E-02 5.1283701E-03 1,midg,midg; igrid,midg,midg -4.6082962E-02 2.8828831E-02 gauss-seidel spectral radius is 0.9985884 estimated iterations to convergence 211 setup time was (sec) 0.6700000 now iterating at: 14:34:08 rms-change max change #iterations 4.255862 162.5986 at 10iterations 1.962938 63.28946 at 20iterations 0.9069919 28.82422 at 30iterations 0.4187867 15.67388 at 40iterations 0.1934240 5.797487 at 50iterations 8.9024186E-02 2.884349 at 60iterations 4.1119654E-02 1.380486 at 70iterations 1.8994449E-02 0.5857664 at 80iterations 8.7938467E-03 0.2637272 at 90iterations 4.0712939E-03 0.1401672 at 100iterations 1.8827292E-03 5.9711933E-02 at 110iterations 8.7483064E-04 2.6831388E-02 at 120iterations finished qdiffx linear iterations at : 14:34:22 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 8.7483064E-04 2.6831388E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.810000 DelPhi exited at 14:34:23 8.809u 0.282s 0:16.17 56.1% 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 Sat Oct 15 2011 at 14:34:24 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2830 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.773546 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): -9.115000 48.64500 ymin,ymax (A): -8.374001 38.66200 zmin,zma (A): 0.4230000 54.90100 x,y,z range (A): 57.76000 47.03600 54.47800 scale (grids/A): 2.773546 object centre (A): 19.76500 15.14400 27.66200 number of atom coordinates read : 2830 total number of charged atoms : 2689 net assigned charge : -1.985968 assigned positive charge : 428.4651 centred at (gu) : 86.70385 88.73695 85.35532 assigned negative charge : -430.4522 centred at (gu) : 86.35499 88.34106 85.19930 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 183215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26661 grid for indexing accessible points = 1.400000 m= 87823 mr = 130087 m= 29088 mr = 69970 m= 6455 mr = 22583 m= 796 mr = 4562 m= 35 mr = 505 m= 0 mr = 13 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3026 time to turn everything in is 1.000000 number of dielectric boundary points 79692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 21510 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) : 1.849030 object centre at (A) : 19.76500 15.14400 27.66200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1256209 -0.2097767 midg,1,midg; midg,igrid,midg -0.1641827 5.4154348E-02 1,midg,midg; igrid,midg,midg -0.5907071 0.4064208 gauss-seidel spectral radius is 0.9992692 estimated iterations to convergence 292 setup time was (sec) 1.280000 now iterating at: 14:34:26 rms-change max change #iterations 10.37366 429.0719 at 10iterations 6.176326 169.5076 at 20iterations 3.644946 87.07769 at 30iterations 2.136114 66.08529 at 40iterations 1.244523 26.57462 at 50iterations 0.7261713 15.92113 at 60iterations 0.4220015 8.272463 at 70iterations 0.2445136 4.849017 at 80iterations 0.1421463 2.791458 at 90iterations 8.2028069E-02 1.645752 at 100iterations 4.7627248E-02 0.9118099 at 110iterations 2.7466152E-02 0.5461140 at 120iterations 1.5866695E-02 0.3121710 at 130iterations 9.1959443E-03 0.1798286 at 140iterations 5.2988785E-03 0.1021423 at 150iterations 3.0597935E-03 5.7463169E-02 at 160iterations 1.7637160E-03 3.4363031E-02 at 170iterations 1.0209553E-03 1.8393993E-02 at 180iterations finished qdiffx linear iterations at : 14:34:47 total time elapsed so far: 14.43000 # loops : 180 mean,max change (kT/e) : 1.0209553E-03 1.8393993E-02 energy calculations done at 14.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 14:34:48 14.571u 0.310s 0:24.00 62.0% 0+0k 0+0io 0pf+0w