Tue Oct 11 08:09:27 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 08:09:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 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: 0.6390350 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): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 0.6390350 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 345.6724 centred at (gu) : 90.38873 87.77632 91.94402 assigned negative charge : -340.1728 centred at (gu) : 90.22656 87.82867 91.88401 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6345 nv = 96 ne = 84 npr = 46479 no. pairs analyzed = 46479 no. exposed pairs = 2962 no. arc points = 20941 no. surface atoms = 990 nbur = 1301 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3331 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2187 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0637183E-09 2.0143270E-08 midg,1,midg; midg,igrid,midg 2.0183473E-08 1.4912900E-09 1,midg,midg; igrid,midg,midg -8.1282190E-09 2.5134137E-08 gauss-seidel spectral radius is 0.9872883 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 08:09:28 rms-change max change #iterations 0.1372128 24.12419 at 10iterations 1.3027113E-02 2.160610 at 20iterations 1.3463643E-03 0.2096596 at 30iterations 1.7764377E-04 3.5129547E-02 at 40iterations 4.3626856E-05 1.0244370E-02 at 50iterations finished qdiffx linear iterations at : 08:09:32 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 4.3626856E-05 1.0244370E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 08:09:33 4.446u 0.400s 0:05.43 89.1% 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 Tue Oct 11 2011 at 08:09:33 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 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: 1.917105 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): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 1.917105 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 345.6724 centred at (gu) : 91.16576 83.32872 95.83179 assigned negative charge : -340.1728 centred at (gu) : 90.67965 83.48582 95.65195 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 68524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20941 grid for indexing accessible points = 1.400000 m= 23550 mr = 46649 m= 3478 mr = 16835 m= 222 mr = 2034 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 232 time to turn everything in is 0.5500000 number of dielectric boundary points 30159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 16945 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) : 0.6390350 object centre at (A) : 2.985500 49.53150 26.66550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1527899E-03 3.2069828E-02 midg,1,midg; midg,igrid,midg 6.2130112E-02 2.3442874E-02 1,midg,midg; igrid,midg,midg -1.1874245E-02 2.3415210E-02 gauss-seidel spectral radius is 0.9986159 estimated iterations to convergence 213 setup time was (sec) 0.8900000 now iterating at: 08:09:34 rms-change max change #iterations 3.965378 166.2462 at 10iterations 1.842362 68.83749 at 20iterations 0.8549755 29.95636 at 30iterations 0.3979339 13.76449 at 40iterations 0.1850166 6.628281 at 50iterations 8.6143747E-02 3.084558 at 60iterations 3.9998338E-02 1.280349 at 70iterations 1.8669957E-02 0.6025772 at 80iterations 8.7272041E-03 0.2724953 at 90iterations 4.0759644E-03 0.1324444 at 100iterations 1.9165640E-03 6.2772751E-02 at 110iterations 9.1377785E-04 3.9880753E-02 at 120iterations finished qdiffx linear iterations at : 08:09:44 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 9.1377785E-04 3.9880753E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 08:09:44 10.562u 0.460s 0:11.33 97.2% 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 08:09:44 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 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: 2.875658 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): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 2.875658 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 345.6724 centred at (gu) : 91.74851 79.99292 98.74773 assigned negative charge : -340.1728 centred at (gu) : 91.01950 80.22869 98.47791 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 158138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20941 grid for indexing accessible points = 1.400000 m= 77326 mr = 113143 m= 26593 mr = 62204 m= 6008 mr = 20723 m= 991 mr = 4386 m= 83 mr = 668 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 1.450000 number of dielectric boundary points 67972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 17231 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) : 1.917105 object centre at (A) : 2.985500 49.53150 26.66550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8489687E-03 0.2997099 midg,1,midg; midg,igrid,midg 0.5969930 0.5296965 1,midg,midg; igrid,midg,midg -8.5654438E-02 0.2248773 gauss-seidel spectral radius is 0.9992568 estimated iterations to convergence 289 setup time was (sec) 1.840000 now iterating at: 08:09:47 rms-change max change #iterations 9.466861 392.3956 at 10iterations 5.557622 147.7283 at 20iterations 3.241310 110.9311 at 30iterations 1.880686 43.81040 at 40iterations 1.090041 24.42049 at 50iterations 0.6296467 13.46198 at 60iterations 0.3628794 8.285836 at 70iterations 0.2094505 4.131393 at 80iterations 0.1203557 2.639561 at 90iterations 6.9259435E-02 1.305266 at 100iterations 3.9927851E-02 0.7385931 at 110iterations 2.2887535E-02 0.5051880 at 120iterations 1.3141957E-02 0.2941284 at 130iterations 7.5656893E-03 0.1456966 at 140iterations 4.3422529E-03 8.6529732E-02 at 150iterations 2.5116929E-03 4.8264980E-02 at 160iterations 1.4495662E-03 3.1036854E-02 at 170iterations 8.4533432E-04 1.6262054E-02 at 180iterations finished qdiffx linear iterations at : 08:10:04 total time elapsed so far: 18.74000 # loops : 180 mean,max change (kT/e) : 8.4533432E-04 1.6262054E-02 energy calculations done at 18.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.91000 DelPhi exited at 08:10:04 18.914u 0.494s 0:19.99 97.0% 0+0k 0+0io 0pf+0w