Sat Oct 8 13:38:18 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 Sat Oct 8 2011 at 13:38:18 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6386223 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): -12.10300 43.64200 ymin,ymax (A): -23.26200 22.61100 zmin,zma (A): -7.646000 46.92400 x,y,z range (A): 55.74500 45.87300 54.57000 scale (grids/A): 0.6386223 object centre (A): 15.76950 -0.3254995 19.63900 number of atom coordinates read : 2983 total number of charged atoms : 2836 net assigned charge : 2.000007 assigned positive charge : 442.5166 centred at (gu) : 88.61699 89.99116 91.82600 assigned negative charge : -440.5173 centred at (gu) : 88.55357 89.91187 91.72312 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8080 nv = 96 ne = 84 npr = 61797 no. pairs analyzed = 61797 no. exposed pairs = 3437 no. arc points = 23968 no. surface atoms = 1172 nbur = 1811 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4686 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9812 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0586021E-09 2.3202873E-08 midg,1,midg; midg,igrid,midg -7.5023108E-09 1.2599071E-08 1,midg,midg; igrid,midg,midg -7.4488198E-09 7.9187510E-09 gauss-seidel spectral radius is 0.9873254 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 13:38:19 rms-change max change #iterations 0.1541216 22.82469 at 10iterations 1.5755534E-02 2.288338 at 20iterations 1.6514095E-03 0.2104721 at 30iterations 1.9813440E-04 3.0929565E-02 at 40iterations 2.9962044E-05 4.3277740E-03 at 50iterations finished qdiffx linear iterations at : 13:38:24 total time elapsed so far: 5.300000 # loops : 50 mean,max change (kT/e) : 2.9962044E-05 4.3277740E-03 energy calculations done at 5.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.480000 DelPhi exited at 13:38:25 5.483u 0.452s 0:06.21 95.4% 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 8 2011 at 13:38:25 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.915867 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): -12.10300 43.64200 ymin,ymax (A): -23.26200 22.61100 zmin,zma (A): -7.646000 46.92400 x,y,z range (A): 55.74500 45.87300 54.57000 scale (grids/A): 1.915867 object centre (A): 15.76950 -0.3254995 19.63900 number of atom coordinates read : 2983 total number of charged atoms : 2836 net assigned charge : 2.000007 assigned positive charge : 442.5166 centred at (gu) : 85.85044 89.97275 95.47715 assigned negative charge : -440.5173 centred at (gu) : 85.66056 89.73537 95.16901 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23968 grid for indexing accessible points = 1.400000 m= 32160 mr = 63203 m= 4955 mr = 24208 m= 302 mr = 3034 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 34791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22319 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) : 0.6386223 object centre at (A) : 15.76950 -0.3254995 19.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4843343E-02 2.0272313E-02 midg,1,midg; midg,igrid,midg 3.8746838E-03 2.0144345E-02 1,midg,midg; igrid,midg,midg -3.7340235E-02 1.5519867E-02 gauss-seidel spectral radius is 0.9986817 estimated iterations to convergence 218 setup time was (sec) 1.070000 now iterating at: 13:38:26 rms-change max change #iterations 4.610555 188.4830 at 10iterations 2.184527 69.11766 at 20iterations 1.038972 33.54761 at 30iterations 0.4948054 14.32863 at 40iterations 0.2349033 6.811386 at 50iterations 0.1117558 3.135175 at 60iterations 5.3121444E-02 1.717830 at 70iterations 2.5211254E-02 0.7704735 at 80iterations 1.1996534E-02 0.3258095 at 90iterations 5.7080914E-03 0.1709900 at 100iterations 2.7082691E-03 7.7333450E-02 at 110iterations 1.2930611E-03 3.6951065E-02 at 120iterations finished qdiffx linear iterations at : 13:38:38 total time elapsed so far: 12.99000 # loops : 120 mean,max change (kT/e) : 1.2930611E-03 3.6951065E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 13:38:39 13.171u 0.513s 0:13.98 97.8% 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 8 2011 at 13:38:39 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.873800 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): -12.10300 43.64200 ymin,ymax (A): -23.26200 22.61100 zmin,zma (A): -7.646000 46.92400 x,y,z range (A): 55.74500 45.87300 54.57000 scale (grids/A): 2.873800 object centre (A): 15.76950 -0.3254995 19.63900 number of atom coordinates read : 2983 total number of charged atoms : 2836 net assigned charge : 2.000007 assigned positive charge : 442.5166 centred at (gu) : 83.77553 89.95918 98.21571 assigned negative charge : -440.5173 centred at (gu) : 83.49070 89.60303 97.75352 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 203854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23968 grid for indexing accessible points = 1.400000 m= 104612 mr = 152916 m= 37223 mr = 87038 m= 8889 mr = 30084 m= 1335 mr = 6621 m= 94 mr = 889 m= 0 mr = 43 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 78416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 22686 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) : 1.915867 object centre at (A) : 15.76950 -0.3254995 19.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3453378E-02 0.2639908 midg,1,midg; midg,igrid,midg 4.2751521E-02 0.2464271 1,midg,midg; igrid,midg,midg -0.5036592 0.1956670 gauss-seidel spectral radius is 0.9992768 estimated iterations to convergence 293 setup time was (sec) 2.320000 now iterating at: 13:38:41 rms-change max change #iterations 10.78396 461.5614 at 10iterations 6.347920 119.4773 at 20iterations 3.722840 78.32943 at 30iterations 2.175079 42.10212 at 40iterations 1.267263 23.33322 at 50iterations 0.7388986 12.58461 at 60iterations 0.4294686 7.810244 at 70iterations 0.2492742 4.149271 at 80iterations 0.1446950 2.666697 at 90iterations 8.3944626E-02 1.369751 at 100iterations 4.8477590E-02 0.7880936 at 110iterations 2.8159985E-02 0.4713936 at 120iterations 1.6323201E-02 0.2698097 at 130iterations 9.4672767E-03 0.1665096 at 140iterations 5.4975674E-03 8.8825226E-02 at 150iterations 3.1877572E-03 5.5358887E-02 at 160iterations 1.8534667E-03 3.2777786E-02 at 170iterations 1.0854141E-03 1.6983032E-02 at 180iterations finished qdiffx linear iterations at : 13:39:01 total time elapsed so far: 21.71000 # loops : 180 mean,max change (kT/e) : 1.0854141E-03 1.6983032E-02 energy calculations done at 21.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.88000 DelPhi exited at 13:39:01 21.882u 0.547s 0:22.72 98.6% 0+0k 0+0io 0pf+0w