Sat Oct 15 13:55:03 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 Sat Oct 15 2011 at 13:55:03 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6324279 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 0.6324279 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1839 net assigned charge : -3.999986 assigned positive charge : 285.4793 centred at (gu) : 88.06694 89.89185 90.47477 assigned negative charge : -289.4791 centred at (gu) : 87.95242 90.04472 90.45037 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5306 nv = 96 ne = 84 npr = 41006 no. pairs analyzed = 41006 no. exposed pairs = 2593 no. arc points = 18795 no. surface atoms = 879 nbur = 1091 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 251 mr = 2663 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1748 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6141372E-09 -3.0547485E-09 midg,1,midg; midg,igrid,midg 6.2317391E-09 -1.5056891E-08 1,midg,midg; igrid,midg,midg -1.9299167E-08 2.2035858E-09 gauss-seidel spectral radius is 0.9869992 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 13:55:04 rms-change max change #iterations 0.1263301 23.48601 at 10iterations 1.2255416E-02 2.090309 at 20iterations 1.1365183E-03 0.1786571 at 30iterations 1.0798885E-04 1.8863678E-02 at 40iterations 1.0477150E-05 2.0160675E-03 at 50iterations finished qdiffx linear iterations at : 13:55:07 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.0477150E-05 2.0160675E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 13:55:08 3.957u 0.242s 0:04.48 93.5% 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 Sat Oct 15 2011 at 13:55:08 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897284 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 1.897284 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1839 net assigned charge : -3.999986 assigned positive charge : 285.4793 centred at (gu) : 84.20109 89.67590 91.42430 assigned negative charge : -289.4791 centred at (gu) : 83.85727 90.13412 91.35125 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 56667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18795 grid for indexing accessible points = 1.400000 m= 18010 mr = 37012 m= 2325 mr = 12466 m= 112 mr = 1326 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1195 time to turn everything in is 0.3000000 number of dielectric boundary points 26272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14455 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) : 0.6324279 object centre at (A) : 0.6895008 17.51900 53.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5990256E-02 -2.2322165E-02 midg,1,midg; midg,igrid,midg 4.7080447E-03 -1.0221769E-02 1,midg,midg; igrid,midg,midg -2.4551206E-04 2.0778982E-02 gauss-seidel spectral radius is 0.9985669 estimated iterations to convergence 209 setup time was (sec) 0.5700000 now iterating at: 13:55:09 rms-change max change #iterations 3.621927 184.2690 at 10iterations 1.662838 62.80788 at 20iterations 0.7615883 28.64989 at 30iterations 0.3490787 13.06496 at 40iterations 0.1607000 5.997471 at 50iterations 7.3737726E-02 2.595484 at 60iterations 3.3702150E-02 1.376278 at 70iterations 1.5515819E-02 0.5368977 at 80iterations 7.0976131E-03 0.2651482 at 90iterations 3.2719537E-03 0.1128750 at 100iterations 1.4930973E-03 5.5179596E-02 at 110iterations 6.8784441E-04 2.4265289E-02 at 120iterations finished qdiffx linear iterations at : 13:55:17 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 6.8784441E-04 2.4265289E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 13:55:18 9.041u 0.286s 0:09.76 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 15 2011 at 13:55:18 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.845926 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 2.845926 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1839 net assigned charge : -3.999986 assigned positive charge : 285.4793 centred at (gu) : 81.30167 89.51385 92.13641 assigned negative charge : -289.4791 centred at (gu) : 80.78600 90.20116 92.02680 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 131351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18795 grid for indexing accessible points = 1.400000 m= 60152 mr = 90632 m= 19197 mr = 47281 m= 3889 mr = 14821 m= 463 mr = 2730 m= 23 mr = 300 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 4207 time to turn everything in is 0.7800000 number of dielectric boundary points 59308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14707 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) : 1.897284 object centre at (A) : 0.6895008 17.51900 53.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6665910 -0.2847175 midg,1,midg; midg,igrid,midg 2.5749380E-02 -7.1486883E-02 1,midg,midg; igrid,midg,midg -0.2735246 0.3317751 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.080000 now iterating at: 13:55:19 rms-change max change #iterations 8.574832 344.5984 at 10iterations 4.961071 126.9634 at 20iterations 2.858328 61.28971 at 30iterations 1.644591 38.65844 at 40iterations 0.9434847 22.11302 at 50iterations 0.5393646 11.80939 at 60iterations 0.3087037 7.393456 at 70iterations 0.1756447 3.714314 at 80iterations 0.1004350 2.134520 at 90iterations 5.7195149E-02 1.119709 at 100iterations 3.2618444E-02 0.6625538 at 110iterations 1.8567013E-02 0.3870392 at 120iterations 1.0579381E-02 0.2516546 at 130iterations 6.0232338E-03 0.1227417 at 140iterations 3.4315479E-03 7.0262909E-02 at 150iterations 1.9495201E-03 3.9501190E-02 at 160iterations 1.1101974E-03 2.3700714E-02 at 170iterations 6.3433399E-04 1.3877153E-02 at 180iterations finished qdiffx linear iterations at : 13:55:32 total time elapsed so far: 14.44000 # loops : 180 mean,max change (kT/e) : 6.3433399E-04 1.3877153E-02 energy calculations done at 14.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.58000 DelPhi exited at 13:55:33 14.584u 0.278s 0:15.17 97.8% 0+0k 0+0io 0pf+0w