Tue Oct 11 03:21:56 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 03:21:56 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 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: 0.7238568 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): 18.46300 64.02900 ymin,ymax (A): -10.98900 34.07100 zmin,zma (A): 0.2840000 49.46500 x,y,z range (A): 45.56600 45.06000 49.18100 scale (grids/A): 0.7238568 object centre (A): 41.24600 11.54100 24.87450 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 267.4172 centred at (gu) : 91.13892 90.65744 90.25331 assigned negative charge : -260.4174 centred at (gu) : 91.22829 91.08719 90.29389 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6477 nv = 96 ne = 84 npr = 35042 no. pairs analyzed = 35042 no. exposed pairs = 2416 no. arc points = 17090 no. surface atoms = 813 nbur = 984 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3400 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.1500000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1419 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0802575E-07 6.8509934E-08 midg,1,midg; midg,igrid,midg 2.9289581E-07 -1.9958142E-07 1,midg,midg; igrid,midg,midg 1.1442705E-07 4.4027114E-08 gauss-seidel spectral radius is 0.9900274 estimated iterations to convergence 81 setup time was (sec) 0.3400000 now iterating at: 03:21:57 rms-change max change #iterations 0.2036157 42.44644 at 10iterations 2.5577853E-02 3.547700 at 20iterations 3.2823691E-03 0.4795361 at 30iterations 4.2492853E-04 6.3057899E-02 at 40iterations 5.3412714E-05 8.1748962E-03 at 50iterations finished qdiffx linear iterations at : 03:22:00 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.3412714E-05 8.1748962E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 03:22:00 3.318u 0.169s 0:03.80 91.3% 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 03:22:00 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 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: 2.171570 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): 18.46300 64.02900 ymin,ymax (A): -10.98900 34.07100 zmin,zma (A): 0.2840000 49.46500 x,y,z range (A): 45.56600 45.06000 49.18100 scale (grids/A): 2.171570 object centre (A): 41.24600 11.54100 24.87450 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 267.4172 centred at (gu) : 93.41666 91.97255 90.76013 assigned negative charge : -260.4174 centred at (gu) : 93.68512 93.26192 90.88201 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67567 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17090 grid for indexing accessible points = 1.400000 m= 26540 mr = 44948 m= 4937 mr = 19606 m= 497 mr = 2933 m= 22 mr = 221 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1126 time to turn everything in is 0.3400000 number of dielectric boundary points 31853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12978 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) : 0.7238568 object centre at (A) : 41.24600 11.54100 24.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3216156E-02 6.2088952E-03 midg,1,midg; midg,igrid,midg 8.1785358E-02 -9.4324671E-02 1,midg,midg; igrid,midg,midg 2.3815356E-02 5.9254620E-02 gauss-seidel spectral radius is 0.9988596 estimated iterations to convergence 234 setup time was (sec) 0.5500000 now iterating at: 03:22:01 rms-change max change #iterations 4.420247 221.8430 at 10iterations 2.205342 87.22732 at 20iterations 1.097030 39.01407 at 30iterations 0.5475457 20.55513 at 40iterations 0.2737128 9.457867 at 50iterations 0.1367481 4.161385 at 60iterations 6.7984968E-02 2.008804 at 70iterations 3.3999242E-02 1.037672 at 80iterations 1.6908396E-02 0.5301818 at 90iterations 8.4428545E-03 0.2655811 at 100iterations 4.2203297E-03 0.1296842 at 110iterations 2.1136578E-03 6.9674015E-02 at 120iterations finished qdiffx linear iterations at : 03:22:08 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.1136578E-03 6.9674015E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 03:22:08 7.711u 0.202s 0:08.20 96.4% 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 Tue Oct 11 2011 at 03:22:08 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 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: 3.257355 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): 18.46300 64.02900 ymin,ymax (A): -10.98900 34.07100 zmin,zma (A): 0.2840000 49.46500 x,y,z range (A): 45.56600 45.06000 49.18100 scale (grids/A): 3.257355 object centre (A): 41.24600 11.54100 24.87450 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 267.4172 centred at (gu) : 95.12505 92.95876 91.14008 assigned negative charge : -260.4174 centred at (gu) : 95.52790 94.89292 91.32305 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17090 grid for indexing accessible points = 1.400000 m= 81492 mr = 108740 m= 33556 mr = 66272 m= 8993 mr = 27026 m= 1818 mr = 6449 m= 295 mr = 1196 m= 22 mr = 192 m= 0 mr = 5 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4083 time to turn everything in is 1.040000 number of dielectric boundary points 71774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 13048 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) : 2.171570 object centre at (A) : 41.24600 11.54100 24.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3020736 -6.7120701E-02 midg,1,midg; midg,igrid,midg 0.4804786 -1.043749 1,midg,midg; igrid,midg,midg 0.1155996 0.7012627 gauss-seidel spectral radius is 0.9993193 estimated iterations to convergence 302 setup time was (sec) 1.280000 now iterating at: 03:22:10 rms-change max change #iterations 9.977274 312.1819 at 10iterations 6.022896 152.7170 at 20iterations 3.608194 82.41884 at 30iterations 2.147195 43.49081 at 40iterations 1.275416 24.76077 at 50iterations 0.7587354 13.75322 at 60iterations 0.4478062 8.600666 at 70iterations 0.2641777 5.162888 at 80iterations 0.1562958 3.029110 at 90iterations 9.2030413E-02 1.727292 at 100iterations 5.4285031E-02 1.040451 at 110iterations 3.1981423E-02 0.5505904 at 120iterations 1.8799637E-02 0.3178139 at 130iterations 1.1059063E-02 0.2241441 at 140iterations 6.5065064E-03 0.1206894 at 150iterations 3.8222068E-03 6.7951202E-02 at 160iterations 2.2469545E-03 3.9253235E-02 at 170iterations 1.3216545E-03 2.3097277E-02 at 180iterations finished qdiffx linear iterations at : 03:22:21 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 1.3216545E-03 2.3097277E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 03:22:21 12.619u 0.203s 0:13.26 96.6% 0+0k 0+0io 0pf+0w