Mon Oct 10 14:41:17 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 Mon Oct 10 2011 at 14:41:17 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5828517 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): -8.481000 52.59800 ymin,ymax (A): -16.01900 34.16600 zmin,zma (A): 77.40600 130.5170 x,y,z range (A): 61.07900 50.18500 53.11102 scale (grids/A): 0.5828517 object centre (A): 22.05850 9.073500 103.9615 number of atom coordinates read : 2736 total number of charged atoms : 2594 net assigned charge : -1.099990 assigned positive charge : 428.5364 centred at (gu) : 92.26183 89.80295 89.27851 assigned negative charge : -429.6373 centred at (gu) : 92.16769 89.92308 89.37276 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6225 nv = 96 ne = 84 npr = 53251 no. pairs analyzed = 53251 no. exposed pairs = 3720 no. arc points = 26062 no. surface atoms = 1257 nbur = 1479 mkacc time = 0.1400000 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 = 1.484000 m= 281 mr = 3104 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2756 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1722866E-09 -2.1556097E-09 midg,1,midg; midg,igrid,midg 2.5298197E-09 -3.0271536E-09 1,midg,midg; igrid,midg,midg -1.5064490E-09 3.1566703E-09 gauss-seidel spectral radius is 0.9847903 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 14:41:18 rms-change max change #iterations 0.1010938 15.48573 at 10iterations 7.9470882E-03 1.308441 at 20iterations 7.0695108E-04 0.1229782 at 30iterations 1.0757088E-04 1.9666672E-02 at 40iterations 2.6447391E-05 5.1364899E-03 at 50iterations finished qdiffx linear iterations at : 14:41:22 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 2.6447391E-05 5.1364899E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 14:41:23 4.870u 0.397s 0:05.63 93.4% 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 Mon Oct 10 2011 at 14:41:23 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.748555 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): -8.481000 52.59800 ymin,ymax (A): -16.01900 34.16600 zmin,zma (A): 77.40600 130.5170 x,y,z range (A): 61.07900 50.18500 53.11102 scale (grids/A): 1.748555 object centre (A): 22.05850 9.073500 103.9615 number of atom coordinates read : 2736 total number of charged atoms : 2594 net assigned charge : -1.099990 assigned positive charge : 428.5364 centred at (gu) : 96.78461 89.40801 87.83476 assigned negative charge : -429.6373 centred at (gu) : 96.50287 89.76895 88.11770 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26062 grid for indexing accessible points = 1.400000 m= 22295 mr = 45012 m= 2873 mr = 15169 m= 119 mr = 1401 m= 0 mr = 23 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20158 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) : 0.5828517 object centre at (A) : 22.05850 9.073500 103.9615 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4458437E-03 -2.8842859E-02 midg,1,midg; midg,igrid,midg 1.1304500E-02 -1.5772253E-02 1,midg,midg; igrid,midg,midg 1.7540127E-02 4.3576743E-02 gauss-seidel spectral radius is 0.9984102 estimated iterations to convergence 199 setup time was (sec) 1.000000 now iterating at: 14:41:24 rms-change max change #iterations 3.831124 180.3869 at 10iterations 1.675799 59.83089 at 20iterations 0.7390241 25.69685 at 30iterations 0.3242964 12.49253 at 40iterations 0.1433149 5.139825 at 50iterations 6.2602691E-02 2.199072 at 60iterations 2.7730409E-02 0.8905411 at 70iterations 1.2284420E-02 0.4280643 at 80iterations 5.4059825E-03 0.1916885 at 90iterations 2.3973971E-03 8.8308334E-02 at 100iterations 1.0679888E-03 3.6613464E-02 at 110iterations 4.8007368E-04 1.8742085E-02 at 120iterations finished qdiffx linear iterations at : 14:41:35 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 4.8007368E-04 1.8742085E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 14:41:39 12.038u 0.439s 0:16.27 76.5% 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 Mon Oct 10 2011 at 14:41:39 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 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: 2.622833 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): -8.481000 52.59800 ymin,ymax (A): -16.01900 34.16600 zmin,zma (A): 77.40600 130.5170 x,y,z range (A): 61.07900 50.18500 53.11102 scale (grids/A): 2.622833 object centre (A): 22.05850 9.073500 103.9615 number of atom coordinates read : 2736 total number of charged atoms : 2594 net assigned charge : -1.099990 assigned positive charge : 428.5364 centred at (gu) : 100.1768 89.11196 86.75191 assigned negative charge : -429.6373 centred at (gu) : 99.75439 89.65340 87.17642 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 156635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26062 grid for indexing accessible points = 1.400000 m= 74370 mr = 110133 m= 23822 mr = 58062 m= 4653 mr = 17729 m= 557 mr = 3102 m= 16 mr = 301 m= 0 mr = 5 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 70721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 20742 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) : 1.748555 object centre at (A) : 22.05850 9.073500 103.9615 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9504619E-02 -0.3767006 midg,1,midg; midg,igrid,midg 0.1546805 -0.1766254 1,midg,midg; igrid,midg,midg 0.3453846 0.4936142 gauss-seidel spectral radius is 0.9992037 estimated iterations to convergence 280 setup time was (sec) 1.770000 now iterating at: 14:41:41 rms-change max change #iterations 9.597432 285.0811 at 10iterations 5.563958 160.5436 at 20iterations 3.195000 72.58960 at 30iterations 1.826401 41.49655 at 40iterations 1.038448 21.23943 at 50iterations 0.5898244 12.26869 at 60iterations 0.3336580 8.000759 at 70iterations 0.1886473 4.055964 at 80iterations 0.1068739 2.108234 at 90iterations 6.0275976E-02 1.217061 at 100iterations 3.4006223E-02 0.7964573 at 110iterations 1.9174248E-02 0.3999562 at 120iterations 1.0806597E-02 0.2589512 at 130iterations 6.0890294E-03 0.1277924 at 140iterations 3.4300340E-03 8.0734253E-02 at 150iterations 1.9406884E-03 4.2541504E-02 at 160iterations 1.0975320E-03 2.2304535E-02 at 170iterations 6.2428234E-04 1.3013601E-02 at 180iterations finished qdiffx linear iterations at : 14:41:59 total time elapsed so far: 18.95000 # loops : 180 mean,max change (kT/e) : 6.2428234E-04 1.3013601E-02 energy calculations done at 18.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.12000 DelPhi exited at 14:41:59 19.129u 0.484s 0:20.01 97.9% 0+0k 0+0io 0pf+0w