Mon Oct 10 09:43:59 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 Mon Oct 10 2011 at 09:43:59 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 = 2809 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: 0.5688446 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): -18.48000 34.25600 ymin,ymax (A): -62.94300 -0.9120001 zmin,zma (A): -1.922000 60.66100 x,y,z range (A): 52.73600 62.03100 62.58300 scale (grids/A): 0.5688446 object centre (A): 7.887999 -31.92750 29.36950 number of atom coordinates read : 2809 total number of charged atoms : 2659 net assigned charge : 7.000012 assigned positive charge : 409.6349 centred at (gu) : 89.04266 88.61074 87.87556 assigned negative charge : -402.6354 centred at (gu) : 89.14468 88.44658 87.81114 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6253 nv = 96 ne = 84 npr = 53548 no. pairs analyzed = 53548 no. exposed pairs = 4285 no. arc points = 31345 no. surface atoms = 1421 nbur = 1388 mkacc time = 0.1300000 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 = 1.540000 m= 313 mr = 2700 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3065 ## 372 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6858360E-10 1.1759134E-09 midg,1,midg; midg,igrid,midg -1.7155576E-09 2.3351256E-09 1,midg,midg; igrid,midg,midg 3.0541103E-09 -2.5620364E-10 gauss-seidel spectral radius is 0.9840625 estimated iterations to convergence 65 setup time was (sec) 0.5600000 now iterating at: 09:44:00 rms-change max change #iterations 8.2612924E-02 14.34936 at 10iterations 5.9705428E-03 0.9604359 at 20iterations 4.8915797E-04 8.9393139E-02 at 30iterations 6.5475433E-05 9.3746185E-03 at 40iterations 1.5132803E-05 1.8343925E-03 at 50iterations finished qdiffx linear iterations at : 09:44:02 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.5132803E-05 1.8343925E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:44:03 3.381u 0.151s 0:03.81 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 Mon Oct 10 2011 at 09:44:03 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 = 2809 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: 1.706534 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): -18.48000 34.25600 ymin,ymax (A): -62.94300 -0.9120001 zmin,zma (A): -1.922000 60.66100 x,y,z range (A): 52.73600 62.03100 62.58300 scale (grids/A): 1.706534 object centre (A): 7.887999 -31.92750 29.36950 number of atom coordinates read : 2809 total number of charged atoms : 2659 net assigned charge : 7.000012 assigned positive charge : 409.6349 centred at (gu) : 87.12765 85.83192 83.62640 assigned negative charge : -402.6354 centred at (gu) : 87.43375 85.33923 83.43285 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 66549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31345 grid for indexing accessible points = 1.400000 m= 21360 mr = 40266 m= 2821 mr = 13573 m= 105 mr = 1244 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20629 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) : 0.5688446 object centre at (A) : 7.887999 -31.92750 29.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3475014E-03 5.0712735E-03 midg,1,midg; midg,igrid,midg 1.1524975E-02 3.4675561E-02 1,midg,midg; igrid,midg,midg 9.8562054E-03 3.7830998E-03 gauss-seidel spectral radius is 0.9983504 estimated iterations to convergence 195 setup time was (sec) 0.8700000 now iterating at: 09:44:04 rms-change max change #iterations 3.463373 157.7287 at 10iterations 1.494212 54.76618 at 20iterations 0.6487201 27.17461 at 30iterations 0.2802565 9.672907 at 40iterations 0.1212568 4.597301 at 50iterations 5.2792117E-02 1.935181 at 60iterations 2.2919230E-02 0.8520088 at 70iterations 9.9187447E-03 0.3940105 at 80iterations 4.3167109E-03 0.1609545 at 90iterations 1.8755714E-03 6.6417694E-02 at 100iterations 8.1739813E-04 2.9785156E-02 at 110iterations 3.6111029E-04 1.2128115E-02 at 120iterations finished qdiffx linear iterations at : 09:44:10 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 3.6111029E-04 1.2128115E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 09:44:11 7.533u 0.172s 0:08.27 93.1% 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 Mon Oct 10 2011 at 09:44:11 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 = 2809 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: 2.559801 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): -18.48000 34.25600 ymin,ymax (A): -62.94300 -0.9120001 zmin,zma (A): -1.922000 60.66100 x,y,z range (A): 52.73600 62.03100 62.58300 scale (grids/A): 2.559801 object centre (A): 7.887999 -31.92750 29.36950 number of atom coordinates read : 2809 total number of charged atoms : 2659 net assigned charge : 7.000012 assigned positive charge : 409.6349 centred at (gu) : 85.69138 83.74767 80.43948 assigned negative charge : -402.6354 centred at (gu) : 86.15057 83.00880 80.14922 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31345 grid for indexing accessible points = 1.400000 m= 69680 mr = 99742 m= 23057 mr = 51852 m= 4422 mr = 16426 m= 390 mr = 2592 m= 12 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 80655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 21263 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) : 1.706534 object centre at (A) : 7.887999 -31.92750 29.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2032460 8.2633689E-02 midg,1,midg; midg,igrid,midg 0.1538953 0.4177325 1,midg,midg; igrid,midg,midg 6.1101720E-02 4.0904991E-02 gauss-seidel spectral radius is 0.9992039 estimated iterations to convergence 280 setup time was (sec) 1.570000 now iterating at: 09:44:13 rms-change max change #iterations 9.100975 350.6013 at 10iterations 5.371389 150.5534 at 20iterations 3.118860 100.5642 at 30iterations 1.803606 50.78875 at 40iterations 1.033446 27.39465 at 50iterations 0.5903945 14.70337 at 60iterations 0.3367328 8.734291 at 70iterations 0.1914619 5.347397 at 80iterations 0.1087646 2.437564 at 90iterations 6.1489493E-02 1.564117 at 100iterations 3.4839828E-02 0.8783855 at 110iterations 1.9679466E-02 0.4315128 at 120iterations 1.1118076E-02 0.2916527 at 130iterations 6.2698447E-03 0.1404011 at 140iterations 3.5314653E-03 7.7672958E-02 at 150iterations 1.9933067E-03 4.4887543E-02 at 160iterations 1.1227867E-03 2.5135040E-02 at 170iterations 6.3218561E-04 1.4103174E-02 at 180iterations finished qdiffx linear iterations at : 09:44:23 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 6.3218561E-04 1.4103174E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 09:44:24 11.977u 0.190s 0:12.70 95.7% 0+0k 0+0io 0pf+0w