Sun Oct 9 06:48:04 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 Sun Oct 9 2011 at 06:48:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6730442 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): -24.57900 26.05500 ymin,ymax (A): 1.401000 46.06700 zmin,zma (A): -23.41800 29.47600 x,y,z range (A): 50.63400 44.66600 52.89400 scale (grids/A): 0.6730442 object centre (A): 0.7379999 23.73400 3.028999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.0390 centred at (gu) : 89.24001 89.50396 88.63287 assigned negative charge : -300.5391 centred at (gu) : 89.19746 89.72427 88.58640 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6075 nv = 96 ne = 84 npr = 41911 no. pairs analyzed = 41911 no. exposed pairs = 2465 no. arc points = 17613 no. surface atoms = 836 nbur = 1158 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3320 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.1600000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1657 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4928061E-08 5.5425370E-10 midg,1,midg; midg,igrid,midg 4.0814758E-08 -5.1228877E-08 1,midg,midg; igrid,midg,midg -2.1010303E-08 -2.4153924E-11 gauss-seidel spectral radius is 0.9884996 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 06:48:04 rms-change max change #iterations 0.1631800 32.19763 at 10iterations 1.7886497E-02 2.298689 at 20iterations 1.9846370E-03 0.2661028 at 30iterations 2.1992959E-04 3.0494690E-02 at 40iterations 2.4162353E-05 3.2863617E-03 at 50iterations finished qdiffx linear iterations at : 06:48:07 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.4162353E-05 3.2863617E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:48:08 3.359u 0.183s 0:03.81 92.6% 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 06:48:08 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.019133 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): -24.57900 26.05500 ymin,ymax (A): 1.401000 46.06700 zmin,zma (A): -23.41800 29.47600 x,y,z range (A): 50.63400 44.66600 52.89400 scale (grids/A): 2.019133 object centre (A): 0.7379999 23.73400 3.028999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.0390 centred at (gu) : 87.71999 88.51196 85.89858 assigned negative charge : -300.5391 centred at (gu) : 87.59253 89.17285 85.75924 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 64967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17613 grid for indexing accessible points = 1.400000 m= 23272 mr = 44788 m= 4099 mr = 17189 m= 323 mr = 2682 m= 8 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1057 time to turn everything in is 0.3200000 number of dielectric boundary points 27890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14699 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) : 0.6730442 object centre at (A) : 0.7379999 23.73400 3.028999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9275223E-02 3.3532463E-02 midg,1,midg; midg,igrid,midg 4.9573589E-02 -3.8935103E-02 1,midg,midg; igrid,midg,midg -4.6457004E-02 -1.3650744E-02 gauss-seidel spectral radius is 0.9987181 estimated iterations to convergence 221 setup time was (sec) 0.5300000 now iterating at: 06:48:09 rms-change max change #iterations 4.160669 206.4920 at 10iterations 1.986478 74.77433 at 20iterations 0.9533787 34.07822 at 30iterations 0.4563752 16.96961 at 40iterations 0.2181110 7.481930 at 50iterations 0.1044577 3.230153 at 60iterations 5.0121803E-02 1.651298 at 70iterations 2.3978172E-02 0.9012604 at 80iterations 1.1511510E-02 0.3676447 at 90iterations 5.5017909E-03 0.1824570 at 100iterations 2.6511233E-03 0.1041033 at 110iterations 1.2672322E-03 4.1187286E-02 at 120iterations finished qdiffx linear iterations at : 06:48:16 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.2672322E-03 4.1187286E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 06:48:16 7.748u 0.206s 0:08.29 95.7% 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 06:48:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 3.028699 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): -24.57900 26.05500 ymin,ymax (A): 1.401000 46.06700 zmin,zma (A): -23.41800 29.47600 x,y,z range (A): 50.63400 44.66600 52.89400 scale (grids/A): 3.028699 object centre (A): 0.7379999 23.73400 3.028999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.0390 centred at (gu) : 86.57986 87.76782 83.84783 assigned negative charge : -300.5391 centred at (gu) : 86.38874 88.75925 83.63889 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 149869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17613 grid for indexing accessible points = 1.400000 m= 74927 mr = 107888 m= 27651 mr = 61508 m= 7615 mr = 22372 m= 1358 mr = 5788 m= 94 mr = 907 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3875 time to turn everything in is 0.8500000 number of dielectric boundary points 63014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14840 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) : 2.019133 object centre at (A) : 0.7379999 23.73400 3.028999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5601731 0.8767201 midg,1,midg; midg,igrid,midg 0.5501692 -0.4214294 1,midg,midg; igrid,midg,midg -0.4183071 -0.1014375 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 1.090000 now iterating at: 06:48:17 rms-change max change #iterations 9.436135 418.5649 at 10iterations 5.444627 131.1861 at 20iterations 3.141928 77.46292 at 30iterations 1.811566 40.52103 at 40iterations 1.044110 20.60328 at 50iterations 0.6005198 11.01213 at 60iterations 0.3462336 6.340788 at 70iterations 0.1984888 3.968651 at 80iterations 0.1146595 2.234921 at 90iterations 6.6066936E-02 1.222878 at 100iterations 3.8088363E-02 0.7313690 at 110iterations 2.1901665E-02 0.4269555 at 120iterations 1.2579555E-02 0.2317443 at 130iterations 7.2514191E-03 0.1380844 at 140iterations 4.1639693E-03 7.4846037E-02 at 150iterations 2.4074425E-03 5.2001953E-02 at 160iterations 1.3856550E-03 2.5923729E-02 at 170iterations 7.9835433E-04 1.5884399E-02 at 180iterations finished qdiffx linear iterations at : 06:48:29 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 7.9835433E-04 1.5884399E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 06:48:29 12.489u 0.212s 0:13.01 97.5% 0+0k 0+0io 0pf+0w