Sun Oct 9 10:42:56 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 10:42:56 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 = 2184 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6303228 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): -1.902000 51.55300 ymin,ymax (A): -25.26700 31.21200 zmin,zma (A): -3.896000 48.36800 x,y,z range (A): 53.45500 56.47900 52.26400 scale (grids/A): 0.6303228 object centre (A): 24.82550 2.972500 22.23600 number of atom coordinates read : 2184 total number of charged atoms : 2047 net assigned charge : 0.5000162 assigned positive charge : 315.5366 centred at (gu) : 89.70935 90.29815 90.46730 assigned negative charge : -315.0374 centred at (gu) : 89.66564 90.17381 90.40762 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5966 nv = 96 ne = 84 npr = 43181 no. pairs analyzed = 43181 no. exposed pairs = 3020 no. arc points = 21188 no. surface atoms = 1009 nbur = 1175 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 3034 m= 0 mr = 35 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7058 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4608489E-09 5.3335434E-09 midg,1,midg; midg,igrid,midg -8.0712912E-09 1.0043387E-08 1,midg,midg; igrid,midg,midg -2.8490665E-09 3.4407199E-09 gauss-seidel spectral radius is 0.9869366 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 10:42:57 rms-change max change #iterations 0.1207774 19.04064 at 10iterations 1.1350114E-02 2.058647 at 20iterations 1.0680730E-03 0.1624765 at 30iterations 1.0206539E-04 1.4627457E-02 at 40iterations 9.7799702E-06 1.7967224E-03 at 50iterations finished qdiffx linear iterations at : 10:43:00 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 9.7799702E-06 1.7967224E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 10:43:00 3.473u 0.195s 0:03.98 91.9% 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 10:43:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2184 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: 1.890968 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): -1.902000 51.55300 ymin,ymax (A): -25.26700 31.21200 zmin,zma (A): -3.896000 48.36800 x,y,z range (A): 53.45500 56.47900 52.26400 scale (grids/A): 1.890968 object centre (A): 24.82550 2.972500 22.23600 number of atom coordinates read : 2184 total number of charged atoms : 2047 net assigned charge : 0.5000162 assigned positive charge : 315.5366 centred at (gu) : 89.12797 90.89392 91.40151 assigned negative charge : -315.0374 centred at (gu) : 88.99718 90.52174 91.22316 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21188 grid for indexing accessible points = 1.400000 m= 21081 mr = 42306 m= 3174 mr = 14622 m= 192 mr = 1964 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 494 time to turn everything in is 0.3300000 number of dielectric boundary points 29614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 16108 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) : 0.6303228 object centre at (A) : 24.82550 2.972500 22.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4326592E-02 3.0745888E-02 midg,1,midg; midg,igrid,midg -1.3352667E-02 2.3567080E-02 1,midg,midg; igrid,midg,midg -2.0820003E-02 4.9962536E-03 gauss-seidel spectral radius is 0.9985862 estimated iterations to convergence 211 setup time was (sec) 0.5700000 now iterating at: 10:43:01 rms-change max change #iterations 3.686492 180.4811 at 10iterations 1.691457 70.13050 at 20iterations 0.7821558 26.98353 at 30iterations 0.3614945 12.93359 at 40iterations 0.1667884 5.990418 at 50iterations 7.6810956E-02 2.849085 at 60iterations 3.5405375E-02 1.175767 at 70iterations 1.6339811E-02 0.5191460 at 80iterations 7.5545600E-03 0.2446780 at 90iterations 3.4916948E-03 0.1240525 at 100iterations 1.6100419E-03 5.5524826E-02 at 110iterations 7.4502762E-04 2.4871826E-02 at 120iterations finished qdiffx linear iterations at : 10:43:09 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 7.4502762E-04 2.4871826E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 10:43:10 8.384u 0.235s 0:09.11 94.5% 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 Sun Oct 9 2011 at 10:43:10 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 = 2184 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.836452 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): -1.902000 51.55300 ymin,ymax (A): -25.26700 31.21200 zmin,zma (A): -3.896000 48.36800 x,y,z range (A): 53.45500 56.47900 52.26400 scale (grids/A): 2.836452 object centre (A): 24.82550 2.972500 22.23600 number of atom coordinates read : 2184 total number of charged atoms : 2047 net assigned charge : 0.5000162 assigned positive charge : 315.5366 centred at (gu) : 88.69193 91.34096 92.10229 assigned negative charge : -315.0374 centred at (gu) : 88.49586 90.78259 91.83477 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21188 grid for indexing accessible points = 1.400000 m= 69135 mr = 103521 m= 23439 mr = 54502 m= 5539 mr = 18145 m= 848 mr = 4159 m= 56 mr = 575 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1645 time to turn everything in is 0.8400000 number of dielectric boundary points 66693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 16373 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) : 1.890968 object centre at (A) : 24.82550 2.972500 22.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1915805 0.3381397 midg,1,midg; midg,igrid,midg -0.1283928 0.2183635 1,midg,midg; igrid,midg,midg -0.2869127 9.2411488E-03 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.100000 now iterating at: 10:43:11 rms-change max change #iterations 8.733490 462.9959 at 10iterations 5.046592 111.5286 at 20iterations 2.894226 71.62560 at 30iterations 1.662497 33.46468 at 40iterations 0.9497659 20.09689 at 50iterations 0.5446157 11.07607 at 60iterations 0.3106665 6.166154 at 70iterations 0.1777482 3.466091 at 80iterations 0.1015729 1.978371 at 90iterations 5.7907809E-02 1.141602 at 100iterations 3.2989744E-02 0.6480064 at 110iterations 1.8875027E-02 0.3660970 at 120iterations 1.0774864E-02 0.2063470 at 130iterations 6.1365436E-03 0.1077881 at 140iterations 3.5066402E-03 6.8317413E-02 at 150iterations 2.0015989E-03 3.8940430E-02 at 160iterations 1.1408690E-03 2.3565292E-02 at 170iterations 6.5272761E-04 1.2783527E-02 at 180iterations finished qdiffx linear iterations at : 10:43:23 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 6.5272761E-04 1.2783527E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 10:43:24 13.358u 0.234s 0:14.00 97.0% 0+0k 0+0io 0pf+0w