Tue Oct 11 07:31:43 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 Tue Oct 11 2011 at 07:31:43 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 = 3239 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5990241 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): 0.3270000 48.89600 ymin,ymax (A): -7.322000 49.11300 zmin,zma (A): 1.312000 60.74200 x,y,z range (A): 48.56900 56.43500 59.43000 scale (grids/A): 0.5990241 object centre (A): 24.61150 20.89550 31.02700 number of atom coordinates read : 3239 total number of charged atoms : 3096 net assigned charge : -0.9999906 assigned positive charge : 487.4598 centred at (gu) : 89.78914 89.01015 90.89484 assigned negative charge : -488.4610 centred at (gu) : 89.72170 88.93195 90.83974 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7713 nv = 96 ne = 84 npr = 66546 no. pairs analyzed = 66546 no. exposed pairs = 3662 no. arc points = 25541 no. surface atoms = 1245 nbur = 1994 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4590 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.4200000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2598 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9714 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3278965E-09 2.5239506E-09 midg,1,midg; midg,igrid,midg -4.9076530E-09 2.4308469E-09 1,midg,midg; igrid,midg,midg -3.5837242E-09 2.4622568E-09 gauss-seidel spectral radius is 0.9856259 estimated iterations to convergence 68 setup time was (sec) 0.7000000 now iterating at: 07:31:44 rms-change max change #iterations 0.1195506 15.69682 at 10iterations 1.0772290E-02 1.276543 at 20iterations 1.0480793E-03 0.1677341 at 30iterations 1.5772664E-04 2.9647827E-02 at 40iterations 3.1283969E-05 6.3686371E-03 at 50iterations finished qdiffx linear iterations at : 07:31:47 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 3.1283969E-05 6.3686371E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 07:31:48 4.229u 0.267s 0:05.22 85.8% 0+0k 0+0io 6pf+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 07:31:48 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 = 3239 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.797072 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): 0.3270000 48.89600 ymin,ymax (A): -7.322000 49.11300 zmin,zma (A): 1.312000 60.74200 x,y,z range (A): 48.56900 56.43500 59.43000 scale (grids/A): 1.797072 object centre (A): 24.61150 20.89550 31.02700 number of atom coordinates read : 3239 total number of charged atoms : 3096 net assigned charge : -0.9999906 assigned positive charge : 487.4598 centred at (gu) : 89.36672 87.02995 92.68365 assigned negative charge : -488.4610 centred at (gu) : 89.16459 86.79559 92.51897 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 84540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25541 grid for indexing accessible points = 1.400000 m= 31409 mr = 61343 m= 4521 mr = 24165 m= 166 mr = 2904 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2543 time to turn everything in is 0.7400000 number of dielectric boundary points 32177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24158 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) : 0.5990241 object centre at (A) : 24.61150 20.89550 31.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8851752E-03 4.6121958E-03 midg,1,midg; midg,igrid,midg -1.9704180E-02 7.0405463E-03 1,midg,midg; igrid,midg,midg -1.5013091E-02 4.1755661E-03 gauss-seidel spectral radius is 0.9985301 estimated iterations to convergence 207 setup time was (sec) 1.040000 now iterating at: 07:31:49 rms-change max change #iterations 4.298398 178.0001 at 10iterations 1.958517 68.62465 at 20iterations 0.8917410 27.46638 at 30iterations 0.4072870 11.96592 at 40iterations 0.1858282 6.122068 at 50iterations 8.5108854E-02 2.582413 at 60iterations 3.8640372E-02 1.133648 at 70iterations 1.7740095E-02 0.5381737 at 80iterations 8.1390971E-03 0.2511492 at 90iterations 3.7329183E-03 0.1195450 at 100iterations 1.7326924E-03 5.6268692E-02 at 110iterations 8.0591848E-04 2.6918411E-02 at 120iterations finished qdiffx linear iterations at : 07:31:58 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 8.0591848E-04 2.6918411E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 07:31:58 9.731u 0.330s 0:10.63 94.6% 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 07:31:59 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 = 3239 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: 2.695608 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): 0.3270000 48.89600 ymin,ymax (A): -7.322000 49.11300 zmin,zma (A): 1.312000 60.74200 x,y,z range (A): 48.56900 56.43500 59.43000 scale (grids/A): 2.695608 object centre (A): 24.61150 20.89550 31.02700 number of atom coordinates read : 3239 total number of charged atoms : 3096 net assigned charge : -0.9999906 assigned positive charge : 487.4598 centred at (gu) : 89.04979 85.54471 94.02515 assigned negative charge : -488.4610 centred at (gu) : 88.74671 85.19310 93.77834 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 195919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25541 grid for indexing accessible points = 1.400000 m= 103168 mr = 147937 m= 36503 mr = 87096 m= 7919 mr = 30109 m= 814 mr = 6084 m= 27 mr = 507 m= 0 mr = 10 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 8755 time to turn everything in is 1.880000 number of dielectric boundary points 72607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 24761 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) : 1.797072 object centre at (A) : 24.61150 20.89550 31.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3134799 -0.1909372 midg,1,midg; midg,igrid,midg -0.3135962 2.8803114E-02 1,midg,midg; igrid,midg,midg -0.2018854 3.0933425E-02 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 2.220000 now iterating at: 07:32:01 rms-change max change #iterations 10.26326 356.5722 at 10iterations 5.912054 113.6187 at 20iterations 3.392169 71.99480 at 30iterations 1.935030 39.46775 at 40iterations 1.107002 19.81966 at 50iterations 0.6333644 11.17127 at 60iterations 0.3609572 6.067032 at 70iterations 0.2057248 3.743141 at 80iterations 0.1172388 2.186134 at 90iterations 6.6878647E-02 1.112766 at 100iterations 3.8104456E-02 0.6684732 at 110iterations 2.1704175E-02 0.3790474 at 120iterations 1.2378984E-02 0.2252703 at 130iterations 7.0527629E-03 0.1265831 at 140iterations 4.0253620E-03 7.0889473E-02 at 150iterations 2.3023607E-03 4.0420532E-02 at 160iterations 1.3204921E-03 2.3157120E-02 at 170iterations 7.6093228E-04 1.4219284E-02 at 180iterations finished qdiffx linear iterations at : 07:32:15 total time elapsed so far: 16.37000 # loops : 180 mean,max change (kT/e) : 7.6093228E-04 1.4219284E-02 energy calculations done at 16.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.55000 DelPhi exited at 07:32:16 16.553u 0.334s 0:17.27 97.7% 0+0k 0+0io 0pf+0w