Sat Oct 15 13:37:39 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 Sat Oct 15 2011 at 13:37:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2158 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: 0.6904711 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): -22.27800 24.56100 ymin,ymax (A): -54.56800 -9.044000 zmin,zma (A): -32.57900 18.98000 x,y,z range (A): 46.83900 45.52400 51.55900 scale (grids/A): 0.6904711 object centre (A): 1.141500 -31.80600 -6.799501 number of atom coordinates read : 2158 total number of charged atoms : 2018 net assigned charge : -5.999979 assigned positive charge : 323.3988 centred at (gu) : 89.27808 90.79347 91.38454 assigned negative charge : -329.3989 centred at (gu) : 89.31413 90.86740 91.56868 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7081 nv = 96 ne = 84 npr = 43217 no. pairs analyzed = 43217 no. exposed pairs = 2838 no. arc points = 20145 no. surface atoms = 955 nbur = 1203 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 3822 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.1800000 number of dielectric boundary points 3671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1783 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3430394E-08 -1.3025371E-07 midg,1,midg; midg,igrid,midg -5.6758074E-09 -6.8520357E-08 1,midg,midg; igrid,midg,midg -2.2368333E-08 -3.9126121E-08 gauss-seidel spectral radius is 0.9890895 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 13:37:39 rms-change max change #iterations 0.1863450 27.62484 at 10iterations 2.1847203E-02 2.713266 at 20iterations 2.5290633E-03 0.3564758 at 30iterations 2.9502538E-04 3.9036751E-02 at 40iterations 3.4629807E-05 4.6024919E-03 at 50iterations finished qdiffx linear iterations at : 13:37:43 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 3.4629807E-05 4.6024919E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 13:37:44 3.995u 0.246s 0:04.98 84.9% 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 13:37:44 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2158 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: 2.071413 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): -22.27800 24.56100 ymin,ymax (A): -54.56800 -9.044000 zmin,zma (A): -32.57900 18.98000 x,y,z range (A): 46.83900 45.52400 51.55900 scale (grids/A): 2.071413 object centre (A): 1.141500 -31.80600 -6.799501 number of atom coordinates read : 2158 total number of charged atoms : 2018 net assigned charge : -5.999979 assigned positive charge : 323.3988 centred at (gu) : 87.83405 92.38027 94.15351 assigned negative charge : -329.3989 centred at (gu) : 87.94241 92.60201 94.70594 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20145 grid for indexing accessible points = 1.400000 m= 28728 mr = 50786 m= 5662 mr = 21410 m= 473 mr = 3842 m= 8 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1242 time to turn everything in is 0.4000000 number of dielectric boundary points 33643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 16021 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) : 0.6904711 object centre at (A) : 1.141500 -31.80600 -6.799501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5840866E-02 -0.1276317 midg,1,midg; midg,igrid,midg -1.5500722E-02 -3.2705698E-02 1,midg,midg; igrid,midg,midg 5.7891090E-03 -1.6127172E-03 gauss-seidel spectral radius is 0.9987992 estimated iterations to convergence 228 setup time was (sec) 0.6900000 now iterating at: 13:37:45 rms-change max change #iterations 4.546877 197.5450 at 10iterations 2.219747 88.01981 at 20iterations 1.087107 35.49286 at 30iterations 0.5313337 16.02295 at 40iterations 0.2610426 7.815394 at 50iterations 0.1275165 3.820179 at 60iterations 6.2796697E-02 1.981773 at 70iterations 3.0734792E-02 1.146231 at 80iterations 1.5096853E-02 0.5288868 at 90iterations 7.3808064E-03 0.2354345 at 100iterations 3.6171726E-03 0.1048393 at 110iterations 1.7753443E-03 5.6655884E-02 at 120iterations finished qdiffx linear iterations at : 13:37:57 total time elapsed so far: 8.690000 # loops : 120 mean,max change (kT/e) : 1.7753443E-03 5.6655884E-02 energy calculations done at 8.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 13:37:57 8.834u 0.301s 0:13.54 67.4% 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 13:37:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2158 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: 3.107120 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): -22.27800 24.56100 ymin,ymax (A): -54.56800 -9.044000 zmin,zma (A): -32.57900 18.98000 x,y,z range (A): 46.83900 45.52400 51.55900 scale (grids/A): 3.107120 object centre (A): 1.141500 -31.80600 -6.799501 number of atom coordinates read : 2158 total number of charged atoms : 2018 net assigned charge : -5.999979 assigned positive charge : 323.3988 centred at (gu) : 86.75110 93.57041 96.23026 assigned negative charge : -329.3989 centred at (gu) : 86.91354 93.90304 97.05877 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 173095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20145 grid for indexing accessible points = 1.400000 m= 89395 mr = 123031 m= 36313 mr = 73115 m= 10495 mr = 29607 m= 2026 mr = 8303 m= 173 mr = 1496 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 4202 time to turn everything in is 1.180000 number of dielectric boundary points 75859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 16144 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) : 2.071413 object centre at (A) : 1.141500 -31.80600 -6.799501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2514339 -1.308111 midg,1,midg; midg,igrid,midg -0.1482071 -0.2298257 1,midg,midg; igrid,midg,midg 6.9742583E-02 -4.2656295E-02 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 1.460000 now iterating at: 13:38:04 rms-change max change #iterations 10.13522 534.0796 at 10iterations 5.931550 145.3565 at 20iterations 3.457808 75.05598 at 30iterations 2.012816 40.64900 at 40iterations 1.173861 20.59916 at 50iterations 0.6833166 15.36950 at 60iterations 0.3975985 7.561907 at 70iterations 0.2312197 4.361902 at 80iterations 0.1345026 2.256061 at 90iterations 7.8337915E-02 1.338312 at 100iterations 4.5455631E-02 0.8141718 at 110iterations 2.6428208E-02 0.4967513 at 120iterations 1.5356230E-02 0.2807999 at 130iterations 8.9452611E-03 0.1646276 at 140iterations 5.1789754E-03 9.8240733E-02 at 150iterations 3.0161960E-03 5.6232452E-02 at 160iterations 1.7497134E-03 3.1237602E-02 at 170iterations 1.0196089E-03 1.7645359E-02 at 180iterations finished qdiffx linear iterations at : 13:38:24 total time elapsed so far: 14.45000 # loops : 180 mean,max change (kT/e) : 1.0196089E-03 1.7645359E-02 energy calculations done at 14.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 13:38:24 14.596u 0.262s 0:25.84 57.4% 0+0k 0+0io 0pf+0w