Sun Oct 9 04:16:40 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+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 04:16:40 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5001757 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): -56.27900 3.536000 ymin,ymax (A): 36.75000 107.9250 zmin,zma (A): 2.116000 66.54800 x,y,z range (A): 59.81500 71.17500 64.43201 scale (grids/A): 0.5001757 object centre (A): -26.37150 72.33749 34.33200 number of atom coordinates read : 3591 total number of charged atoms : 3362 net assigned charge : 5.300037 assigned positive charge : 517.5692 centred at (gu) : 91.83409 94.74203 89.75746 assigned negative charge : -512.2704 centred at (gu) : 91.94679 94.69517 89.74537 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5756 nv = 96 ne = 84 npr = 73341 no. pairs analyzed = 73341 no. exposed pairs = 4581 no. arc points = 32798 no. surface atoms = 1549 nbur = 2042 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 200 mr = 2836 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3041 ## 447 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7556 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3260977E-11 5.5109223E-11 midg,1,midg; midg,igrid,midg -1.7384784E-12 3.6077072E-10 1,midg,midg; igrid,midg,midg 1.0502181E-10 -1.4257354E-10 gauss-seidel spectral radius is 0.9794851 estimated iterations to convergence 58 setup time was (sec) 0.4500000 now iterating at: 04:16:40 rms-change max change #iterations 5.3256813E-02 8.580948 at 10iterations 2.8754361E-03 0.4815845 at 20iterations 3.0351270E-04 6.7077637E-02 at 30iterations 7.9757498E-05 1.4170647E-02 at 40iterations 2.4942899E-05 4.5676231E-03 at 50iterations finished qdiffx linear iterations at : 04:16:43 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.4942899E-05 4.5676231E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 04:16:44 3.462u 0.172s 0:03.95 91.8% 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 Sun Oct 9 2011 at 04:16:44 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.500527 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): -56.27900 3.536000 ymin,ymax (A): 36.75000 107.9250 zmin,zma (A): 2.116000 66.54800 x,y,z range (A): 59.81500 71.17500 64.43201 scale (grids/A): 1.500527 object centre (A): -26.37150 72.33749 34.33200 number of atom coordinates read : 3591 total number of charged atoms : 3362 net assigned charge : 5.300037 assigned positive charge : 517.5692 centred at (gu) : 95.50109 104.2247 89.27089 assigned negative charge : -512.2704 centred at (gu) : 95.83987 104.0853 89.23573 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32798 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 18670 mr = 43262 m= 1548 mr = 12429 m= 21 mr = 650 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.3300000 number of dielectric boundary points 28990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 25160 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) : 0.5001757 object centre at (A) : -26.37150 72.33749 34.33200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6668914E-03 3.7316517E-03 midg,1,midg; midg,igrid,midg -8.2220393E-04 1.4424769E-02 1,midg,midg; igrid,midg,midg 3.9806110E-03 -7.9256771E-03 gauss-seidel spectral radius is 0.9978848 estimated iterations to convergence 173 setup time was (sec) 0.5400000 now iterating at: 04:16:44 rms-change max change #iterations 2.989993 125.3193 at 10iterations 1.161992 45.48521 at 20iterations 0.4524758 16.65998 at 30iterations 0.1756409 6.957229 at 40iterations 6.8639725E-02 2.565444 at 50iterations 2.6758108E-02 1.085590 at 60iterations 1.0463800E-02 0.3997320 at 70iterations 4.1490719E-03 0.1540809 at 80iterations 1.6719172E-03 6.2719345E-02 at 90iterations 7.0524105E-04 2.8154373E-02 at 100iterations 3.3285064E-04 1.4205933E-02 at 110iterations 1.8038788E-04 7.1468353E-03 at 120iterations finished qdiffx linear iterations at : 04:16:51 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.8038788E-04 7.1468353E-03 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 04:16:52 7.640u 0.197s 0:08.12 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 Sun Oct 9 2011 at 04:16:52 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.250790 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): -56.27900 3.536000 ymin,ymax (A): 36.75000 107.9250 zmin,zma (A): 2.116000 66.54800 x,y,z range (A): 59.81500 71.17500 64.43201 scale (grids/A): 2.250790 object centre (A): -26.37150 72.33749 34.33200 number of atom coordinates read : 3591 total number of charged atoms : 3362 net assigned charge : 5.300037 assigned positive charge : 517.5692 centred at (gu) : 98.25127 111.3369 88.90605 assigned negative charge : -512.2704 centred at (gu) : 98.75967 111.1277 88.85339 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 151816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32798 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 65944 mr = 106766 m= 17082 mr = 51128 m= 2107 mr = 12569 m= 86 mr = 1216 m= 0 mr = 30 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.7800000 number of dielectric boundary points 65326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 26808 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) : 1.500527 object centre at (A) : -26.37150 72.33749 34.33200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9523691E-02 5.1802713E-02 midg,1,midg; midg,igrid,midg -2.4336986E-02 0.2207932 1,midg,midg; igrid,midg,midg 5.0020657E-02 -0.1570838 gauss-seidel spectral radius is 0.9990451 estimated iterations to convergence 256 setup time was (sec) 1.020000 now iterating at: 04:16:53 rms-change max change #iterations 8.223535 285.1282 at 10iterations 4.515682 121.1511 at 20iterations 2.464062 61.02496 at 30iterations 1.334855 35.42794 at 40iterations 0.7201222 18.07081 at 50iterations 0.3885440 9.559189 at 60iterations 0.2091325 5.043774 at 70iterations 0.1120384 2.782404 at 80iterations 5.9994735E-02 1.299263 at 90iterations 3.2093074E-02 0.7633924 at 100iterations 1.7175695E-02 0.4226809 at 110iterations 9.1848252E-03 0.1952136 at 120iterations 4.8960275E-03 0.1180258 at 130iterations 2.6198342E-03 5.7313919E-02 at 140iterations 1.3966258E-03 2.9435158E-02 at 150iterations 7.4886961E-04 1.6799450E-02 at 160iterations 4.0303462E-04 8.5692406E-03 at 170iterations 2.1752415E-04 4.7302246E-03 at 180iterations finished qdiffx linear iterations at : 04:17:04 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 2.1752415E-04 4.7302246E-03 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 04:17:05 12.232u 0.197s 0:12.74 97.4% 0+0k 0+0io 0pf+0w