Sun Oct 9 23:24:10 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 Sun Oct 9 2011 at 23:24:10 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2212 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6684943 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): -12.12000 31.32300 ymin,ymax (A): -22.13400 27.47800 zmin,zma (A): -10.54000 42.71400 x,y,z range (A): 43.44300 49.61200 53.25400 scale (grids/A): 0.6684943 object centre (A): 9.601500 2.672000 16.08700 number of atom coordinates read : 2212 total number of charged atoms : 2073 net assigned charge : 1.500009 assigned positive charge : 327.3056 centred at (gu) : 92.11775 91.26543 90.36642 assigned negative charge : -325.8058 centred at (gu) : 92.07042 91.24432 90.06639 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6997 nv = 96 ne = 84 npr = 43028 no. pairs analyzed = 43028 no. exposed pairs = 2945 no. arc points = 20744 no. surface atoms = 988 nbur = 1224 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3749 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1800000 number of dielectric boundary points 3573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4669083E-08 6.8905763E-08 midg,1,midg; midg,igrid,midg 4.3400842E-11 1.1180326E-08 1,midg,midg; igrid,midg,midg -3.4168948E-09 2.1706519E-08 gauss-seidel spectral radius is 0.9883746 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 23:24:11 rms-change max change #iterations 0.1628484 28.11559 at 10iterations 1.7677473E-02 2.514148 at 20iterations 1.9033968E-03 0.2848358 at 30iterations 2.2835255E-04 3.5308838E-02 at 40iterations 4.3599677E-05 7.2870255E-03 at 50iterations finished qdiffx linear iterations at : 23:24:14 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.3599677E-05 7.2870255E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 23:24:14 3.387u 0.167s 0:03.84 92.1% 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 Sun Oct 9 2011 at 23:24:14 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2212 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.005483 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): -12.12000 31.32300 ymin,ymax (A): -22.13400 27.47800 zmin,zma (A): -10.54000 42.71400 x,y,z range (A): 43.44300 49.61200 53.25400 scale (grids/A): 2.005483 object centre (A): 9.601500 2.672000 16.08700 number of atom coordinates read : 2212 total number of charged atoms : 2073 net assigned charge : 1.500009 assigned positive charge : 327.3056 centred at (gu) : 96.35289 93.79620 91.09922 assigned negative charge : -325.8058 centred at (gu) : 96.21109 93.73283 90.19902 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20744 grid for indexing accessible points = 1.400000 m= 27404 mr = 51210 m= 4625 mr = 20051 m= 405 mr = 3007 m= 10 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 174 time to turn everything in is 0.3700000 number of dielectric boundary points 32893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16380 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) : 0.6684943 object centre at (A) : 9.601500 2.672000 16.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8400301E-02 9.5050111E-03 midg,1,midg; midg,igrid,midg 2.2335703E-02 1.8751774E-02 1,midg,midg; igrid,midg,midg -1.2878114E-02 5.1107886E-03 gauss-seidel spectral radius is 0.9987344 estimated iterations to convergence 223 setup time was (sec) 0.5900000 now iterating at: 23:24:15 rms-change max change #iterations 4.267470 171.0087 at 10iterations 2.054356 77.58130 at 20iterations 0.9920843 31.84241 at 30iterations 0.4773747 17.74684 at 40iterations 0.2309998 7.011017 at 50iterations 0.1114451 3.439683 at 60iterations 5.3645805E-02 1.724154 at 70iterations 2.5921661E-02 0.8231735 at 80iterations 1.2470154E-02 0.4157481 at 90iterations 6.0012750E-03 0.1845016 at 100iterations 2.8954218E-03 8.7589264E-02 at 110iterations 1.3978780E-03 5.0453186E-02 at 120iterations finished qdiffx linear iterations at : 23:24:22 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.3978780E-03 5.0453186E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 23:24:22 7.854u 0.198s 0:08.32 96.6% 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 Sun Oct 9 2011 at 23:24:22 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2212 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.008225 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): -12.12000 31.32300 ymin,ymax (A): -22.13400 27.47800 zmin,zma (A): -10.54000 42.71400 x,y,z range (A): 43.44300 49.61200 53.25400 scale (grids/A): 3.008225 object centre (A): 9.601500 2.672000 16.08700 number of atom coordinates read : 2212 total number of charged atoms : 2073 net assigned charge : 1.500009 assigned positive charge : 327.3056 centred at (gu) : 99.52934 95.69429 91.64874 assigned negative charge : -325.8058 centred at (gu) : 99.31659 95.59929 90.29853 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172640 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20744 grid for indexing accessible points = 1.400000 m= 88115 mr = 123645 m= 32337 mr = 71862 m= 8563 mr = 25903 m= 1717 mr = 6582 m= 190 mr = 1314 m= 3 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 0.9800000 number of dielectric boundary points 74118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16584 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) : 2.005483 object centre at (A) : 9.601500 2.672000 16.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5694172 -6.5874554E-02 midg,1,midg; midg,igrid,midg 0.3574802 9.3230335E-03 1,midg,midg; igrid,midg,midg -0.1618969 4.2054225E-02 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 1.220000 now iterating at: 23:24:24 rms-change max change #iterations 9.976445 359.9981 at 10iterations 5.910140 136.0768 at 20iterations 3.498106 74.70890 at 30iterations 2.063299 48.08137 at 40iterations 1.208837 22.94037 at 50iterations 0.7099178 13.15439 at 60iterations 0.4139573 8.120567 at 70iterations 0.2410813 4.615804 at 80iterations 0.1407257 2.832116 at 90iterations 8.2076132E-02 1.552143 at 100iterations 4.7833607E-02 0.8803463 at 110iterations 2.7855804E-02 0.5249901 at 120iterations 1.6205458E-02 0.2871456 at 130iterations 9.4210226E-03 0.1692581 at 140iterations 5.4827724E-03 0.1044846 at 150iterations 3.1835707E-03 6.1080933E-02 at 160iterations 1.8526894E-03 3.2039642E-02 at 170iterations 1.0792533E-03 1.9388199E-02 at 180iterations finished qdiffx linear iterations at : 23:24:35 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.0792533E-03 1.9388199E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 23:24:36 12.756u 0.195s 0:13.22 97.8% 0+0k 0+0io 0pf+0w