Sun Oct 9 23:13:01 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 23:13:01 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6987653 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): -11.99000 31.73200 ymin,ymax (A): -22.31400 28.52900 zmin,zma (A): -9.874001 41.07300 x,y,z range (A): 43.72200 50.84300 50.94700 scale (grids/A): 0.6987653 object centre (A): 9.871000 3.107500 15.59950 number of atom coordinates read : 2169 total number of charged atoms : 2030 net assigned charge : 0.5000094 assigned positive charge : 318.5767 centred at (gu) : 91.99437 90.88869 90.93533 assigned negative charge : -318.0769 centred at (gu) : 91.94492 90.85296 90.64536 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7628 nv = 96 ne = 84 npr = 42062 no. pairs analyzed = 42062 no. exposed pairs = 2829 no. arc points = 20002 no. surface atoms = 963 nbur = 1206 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4219 m= 1 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0054830E-07 1.4246403E-07 midg,1,midg; midg,igrid,midg -1.0877818E-08 1.9638879E-08 1,midg,midg; igrid,midg,midg -1.2538337E-08 3.3013954E-08 gauss-seidel spectral radius is 0.9893505 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 23:13:02 rms-change max change #iterations 0.1928940 28.21050 at 10iterations 2.2851529E-02 2.836595 at 20iterations 2.7772491E-03 0.4630437 at 30iterations 3.7328716E-04 5.8331966E-02 at 40iterations 9.2343740E-05 1.5171289E-02 at 50iterations finished qdiffx linear iterations at : 23:13:05 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 9.2343740E-05 1.5171289E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 23:13:05 3.381u 0.151s 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 23:13:05 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.096296 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): -11.99000 31.73200 ymin,ymax (A): -22.31400 28.52900 zmin,zma (A): -9.874001 41.07300 x,y,z range (A): 43.72200 50.84300 50.94700 scale (grids/A): 2.096296 object centre (A): 9.871000 3.107500 15.59950 number of atom coordinates read : 2169 total number of charged atoms : 2030 net assigned charge : 0.5000094 assigned positive charge : 318.5767 centred at (gu) : 95.98276 92.66589 92.80596 assigned negative charge : -318.0769 centred at (gu) : 95.83459 92.55891 91.93609 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20002 grid for indexing accessible points = 1.400000 m= 32242 mr = 56365 m= 6517 mr = 24559 m= 700 mr = 4515 m= 30 mr = 405 m= 0 mr = 8 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 34704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16116 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) : 0.6987653 object centre at (A) : 9.871000 3.107500 15.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6610824E-02 -1.8377829E-02 midg,1,midg; midg,igrid,midg 3.5781074E-02 6.3593015E-02 1,midg,midg; igrid,midg,midg -1.9321999E-02 -4.2140721E-03 gauss-seidel spectral radius is 0.9988285 estimated iterations to convergence 231 setup time was (sec) 0.9300000 now iterating at: 23:13:06 rms-change max change #iterations 4.589111 260.9354 at 10iterations 2.266283 85.19029 at 20iterations 1.124816 35.83040 at 30iterations 0.5580807 16.49106 at 40iterations 0.2753116 9.060343 at 50iterations 0.1375998 3.971530 at 60iterations 6.7973420E-02 2.282814 at 70iterations 3.3797897E-02 1.025256 at 80iterations 1.6790977E-02 0.5281410 at 90iterations 8.3554657E-03 0.2580109 at 100iterations 4.1748467E-03 0.1338811 at 110iterations 2.1032360E-03 6.6417694E-02 at 120iterations finished qdiffx linear iterations at : 23:13:13 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.1032360E-03 6.6417694E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 23:13:14 7.839u 0.170s 0:08.42 95.0% 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 23:13:14 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.144444 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): -11.99000 31.73200 ymin,ymax (A): -22.31400 28.52900 zmin,zma (A): -9.874001 41.07300 x,y,z range (A): 43.72200 50.84300 50.94700 scale (grids/A): 3.144444 object centre (A): 9.871000 3.107500 15.59950 number of atom coordinates read : 2169 total number of charged atoms : 2030 net assigned charge : 0.5000094 assigned positive charge : 318.5767 centred at (gu) : 98.97398 93.99883 94.20878 assigned negative charge : -318.0769 centred at (gu) : 98.75192 93.83836 92.90402 start vw surface at 0.1500000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 186940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20002 grid for indexing accessible points = 1.400000 m= 100098 mr = 135949 m= 41345 mr = 83181 m= 12478 mr = 34243 m= 2771 mr = 9955 m= 357 mr = 2158 m= 19 mr = 271 m= 0 mr = 5 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 78246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 16240 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) : 2.096296 object centre at (A) : 9.871000 3.107500 15.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6970321 -0.3324640 midg,1,midg; midg,igrid,midg 0.3265781 0.6284976 1,midg,midg; igrid,midg,midg -0.2261674 -6.6646807E-02 gauss-seidel spectral radius is 0.9993130 estimated iterations to convergence 301 setup time was (sec) 2.330000 now iterating at: 23:13:16 rms-change max change #iterations 10.39961 416.7731 at 10iterations 6.220221 136.9723 at 20iterations 3.710073 77.77463 at 30iterations 2.206062 50.31319 at 40iterations 1.306198 27.66200 at 50iterations 0.7748622 13.76725 at 60iterations 0.4585201 7.759838 at 70iterations 0.2699816 5.329276 at 80iterations 0.1593733 3.074444 at 90iterations 9.3745627E-02 1.712605 at 100iterations 5.5153128E-02 0.9068699 at 110iterations 3.2507628E-02 0.5447121 at 120iterations 1.9148342E-02 0.3233080 at 130iterations 1.1251153E-02 0.1888294 at 140iterations 6.6152397E-03 0.1129975 at 150iterations 3.8979056E-03 6.2665462E-02 at 160iterations 2.3135731E-03 4.2057037E-02 at 170iterations 1.3824673E-03 2.2457123E-02 at 180iterations finished qdiffx linear iterations at : 23:13:28 total time elapsed so far: 14.02000 # loops : 180 mean,max change (kT/e) : 1.3824673E-03 2.2457123E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.25000 DelPhi exited at 23:13:28 14.255u 0.242s 0:14.78 98.0% 0+0k 0+0io 0pf+0w