Tue Oct 11 05:27:40 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 05:27:41 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: HIZ 40 has a net charge of 0.2000 !!! WARNING: ZN6 658 has a net charge of 1.4000 !!! WARNING: ZN6 659 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.7048528 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): 17.34200 63.23200 ymin,ymax (A): -3.560000 33.62200 zmin,zma (A): 21.33200 71.83900 x,y,z range (A): 45.89000 37.18200 50.50700 scale (grids/A): 0.7048528 object centre (A): 40.28700 15.03100 46.58550 number of atom coordinates read : 2214 total number of charged atoms : 1951 net assigned charge : 10.00001 assigned positive charge : 318.0170 centred at (gu) : 90.90504 89.64491 88.82409 assigned negative charge : -308.0172 centred at (gu) : 91.04285 89.63523 88.78354 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6919 nv = 96 ne = 84 npr = 39451 no. pairs analyzed = 39451 no. exposed pairs = 2483 no. arc points = 16908 no. surface atoms = 854 nbur = 1360 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 3985 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1631 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7776 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6476667E-08 7.8985266E-08 midg,1,midg; midg,igrid,midg 8.0926554E-08 7.9097006E-08 1,midg,midg; igrid,midg,midg 1.1979135E-07 1.8072319E-08 gauss-seidel spectral radius is 0.9895043 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 05:27:41 rms-change max change #iterations 0.2051164 36.00255 at 10iterations 2.5104310E-02 3.737396 at 20iterations 3.0518791E-03 0.3881607 at 30iterations 3.7103490E-04 6.8937302E-02 at 40iterations 4.6283043E-05 6.2904358E-03 at 50iterations finished qdiffx linear iterations at : 05:27:44 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.6283043E-05 6.2904358E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 05:27:45 3.413u 0.158s 0:04.38 81.2% 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 05:27:45 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: HIZ 40 has a net charge of 0.2000 !!! WARNING: ZN6 658 has a net charge of 1.4000 !!! WARNING: ZN6 659 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: 2.114558 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): 17.34200 63.23200 ymin,ymax (A): -3.560000 33.62200 zmin,zma (A): 21.33200 71.83900 x,y,z range (A): 45.89000 37.18200 50.50700 scale (grids/A): 2.114558 object centre (A): 40.28700 15.03100 46.58550 number of atom coordinates read : 2214 total number of charged atoms : 1951 net assigned charge : 10.00001 assigned positive charge : 318.0170 centred at (gu) : 92.71508 88.93482 86.47224 assigned negative charge : -308.0172 centred at (gu) : 93.12871 88.90578 86.35060 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16908 grid for indexing accessible points = 1.400000 m= 30140 mr = 51773 m= 6094 mr = 23186 m= 500 mr = 4075 m= 5 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.6200000 number of dielectric boundary points 30531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15480 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) : 0.7048528 object centre at (A) : 40.28700 15.03100 46.58550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8954217E-02 5.7063475E-02 midg,1,midg; midg,igrid,midg 2.9810870E-02 2.8014511E-02 1,midg,midg; igrid,midg,midg 4.1201681E-02 3.8745496E-02 gauss-seidel spectral radius is 0.9988191 estimated iterations to convergence 230 setup time was (sec) 0.9100000 now iterating at: 05:27:46 rms-change max change #iterations 4.570137 216.7244 at 10iterations 2.254917 74.19054 at 20iterations 1.118036 39.96540 at 30iterations 0.5533912 16.01607 at 40iterations 0.2733777 9.105482 at 50iterations 0.1356545 4.397728 at 60iterations 6.7276604E-02 1.873373 at 70iterations 3.3212233E-02 0.9691849 at 80iterations 1.6412634E-02 0.5251307 at 90iterations 8.1333164E-03 0.2635612 at 100iterations 4.0399823E-03 0.1281748 at 110iterations 2.0014236E-03 5.7107925E-02 at 120iterations finished qdiffx linear iterations at : 05:27:53 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.0014236E-03 5.7107925E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 05:27:53 7.582u 0.188s 0:08.18 94.8% 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 Tue Oct 11 2011 at 05:27:53 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: HIZ 40 has a net charge of 0.2000 !!! WARNING: ZN6 658 has a net charge of 1.4000 !!! WARNING: ZN6 659 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: 3.171837 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): 17.34200 63.23200 ymin,ymax (A): -3.560000 33.62200 zmin,zma (A): 21.33200 71.83900 x,y,z range (A): 45.89000 37.18200 50.50700 scale (grids/A): 3.171837 object centre (A): 40.28700 15.03100 46.58550 number of atom coordinates read : 2214 total number of charged atoms : 1951 net assigned charge : 10.00001 assigned positive charge : 318.0170 centred at (gu) : 94.07253 88.40225 84.70832 assigned negative charge : -308.0172 centred at (gu) : 94.69307 88.35868 84.52589 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 168006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16908 grid for indexing accessible points = 1.400000 m= 93020 mr = 124469 m= 39126 mr = 77674 m= 11570 mr = 32415 m= 2230 mr = 8988 m= 202 mr = 1652 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 1.830000 number of dielectric boundary points 68854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 15608 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) : 2.114558 object centre at (A) : 40.28700 15.03100 46.58550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5031323 0.4146050 midg,1,midg; midg,igrid,midg 0.2433602 0.2348748 1,midg,midg; igrid,midg,midg 0.3360668 0.5808861 gauss-seidel spectral radius is 0.9992946 estimated iterations to convergence 297 setup time was (sec) 2.130000 now iterating at: 05:27:56 rms-change max change #iterations 10.21833 362.3260 at 10iterations 6.053161 145.0369 at 20iterations 3.585262 77.21107 at 30iterations 2.118135 40.34331 at 40iterations 1.248491 23.74199 at 50iterations 0.7338095 15.40184 at 60iterations 0.4312723 8.396610 at 70iterations 0.2529978 4.590816 at 80iterations 0.1481462 2.660866 at 90iterations 8.6849950E-02 1.576880 at 100iterations 5.0832413E-02 0.9822006 at 110iterations 2.9729124E-02 0.5273542 at 120iterations 1.7396491E-02 0.3169842 at 130iterations 1.0213947E-02 0.1787529 at 140iterations 6.0150828E-03 0.1043720 at 150iterations 3.5677934E-03 6.8288803E-02 at 160iterations 2.1580618E-03 4.2541504E-02 at 170iterations 1.3490625E-03 2.7378082E-02 at 180iterations finished qdiffx linear iterations at : 05:28:06 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.3490625E-03 2.7378082E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 05:28:06 12.589u 0.205s 0:13.09 97.6% 0+0k 0+0io 0pf+0w