Sun Oct 9 16:27:04 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 16:27:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 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: 0.5084915 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): -36.15200 12.00700 ymin,ymax (A): 31.47400 85.15800 zmin,zma (A): -16.80300 53.20800 x,y,z range (A): 48.15900 53.68401 70.01100 scale (grids/A): 0.5084915 object centre (A): -12.07250 58.31600 18.20250 number of atom coordinates read : 3194 total number of charged atoms : 3052 net assigned charge : 2.500008 assigned positive charge : 492.9196 centred at (gu) : 90.30058 88.89988 90.25935 assigned negative charge : -490.4207 centred at (gu) : 90.35640 88.79123 90.15837 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5332 nv = 96 ne = 84 npr = 62287 no. pairs analyzed = 62287 no. exposed pairs = 4261 no. arc points = 30066 no. surface atoms = 1449 nbur = 1745 mkacc time = 0.1000000 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 = 1.680000 m= 155 mr = 2538 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2978 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2291305E-10 2.1045919E-10 midg,1,midg; midg,igrid,midg -1.9547942E-10 1.5578350E-10 1,midg,midg; igrid,midg,midg 1.1498642E-10 -6.1856936E-11 gauss-seidel spectral radius is 0.9801178 estimated iterations to convergence 59 setup time was (sec) 0.4200000 now iterating at: 16:27:05 rms-change max change #iterations 5.1505171E-02 9.028999 at 10iterations 2.8217635E-03 0.5124798 at 20iterations 1.9200987E-04 2.9258728E-02 at 30iterations 2.2390697E-05 2.6245117E-03 at 40iterations 3.7120624E-06 3.9410591E-04 at 50iterations finished qdiffx linear iterations at : 16:27:08 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.7120624E-06 3.9410591E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 16:27:08 3.487u 0.200s 0:04.08 90.1% 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 16:27:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 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: 1.525475 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): -36.15200 12.00700 ymin,ymax (A): 31.47400 85.15800 zmin,zma (A): -16.80300 53.20800 x,y,z range (A): 48.15900 53.68401 70.01100 scale (grids/A): 1.525475 object centre (A): -12.07250 58.31600 18.20250 number of atom coordinates read : 3194 total number of charged atoms : 3052 net assigned charge : 2.500008 assigned positive charge : 492.9196 centred at (gu) : 90.90083 86.69888 90.77738 assigned negative charge : -490.4207 centred at (gu) : 91.06877 86.37354 90.47467 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 60045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30066 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15413 mr = 39048 m= 1115 mr = 9631 m= 25 mr = 376 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 27543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 22826 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) : 0.5084915 object centre at (A) : -12.07250 58.31600 18.20250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2551638E-02 1.0065699E-02 midg,1,midg; midg,igrid,midg -3.1887291E-03 3.3813092E-04 1,midg,midg; igrid,midg,midg 2.0906988E-03 1.9725056E-03 gauss-seidel spectral radius is 0.9979372 estimated iterations to convergence 175 setup time was (sec) 0.5400000 now iterating at: 16:27:09 rms-change max change #iterations 2.977577 166.2225 at 10iterations 1.169969 53.99656 at 20iterations 0.4611270 18.22159 at 30iterations 0.1818795 7.347407 at 40iterations 7.1419127E-02 2.885302 at 50iterations 2.8094202E-02 1.100414 at 60iterations 1.1067430E-02 0.4035692 at 70iterations 4.3604672E-03 0.1724567 at 80iterations 1.7146282E-03 7.4352264E-02 at 90iterations 6.7679962E-04 2.9132843E-02 at 100iterations 2.6821735E-04 1.0973930E-02 at 110iterations 1.0607790E-04 3.7403107E-03 at 120iterations finished qdiffx linear iterations at : 16:27:16 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.0607790E-04 3.7403107E-03 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 16:27:17 7.777u 0.239s 0:08.47 94.4% 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 16:27:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3194 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: 2.288212 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): -36.15200 12.00700 ymin,ymax (A): 31.47400 85.15800 zmin,zma (A): -16.80300 53.20800 x,y,z range (A): 48.15900 53.68401 70.01100 scale (grids/A): 2.288212 object centre (A): -12.07250 58.31600 18.20250 number of atom coordinates read : 3194 total number of charged atoms : 3052 net assigned charge : 2.500008 assigned positive charge : 492.9196 centred at (gu) : 91.35083 85.04800 91.16587 assigned negative charge : -490.4207 centred at (gu) : 91.60294 84.55999 90.71187 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 140106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30066 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 57585 mr = 96564 m= 12330 mr = 43512 m= 1421 mr = 8368 m= 72 mr = 728 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 62333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 24355 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) : 1.525475 object centre at (A) : -12.07250 58.31600 18.20250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2141569 0.1541046 midg,1,midg; midg,igrid,midg -2.7903961E-02 -5.4868022E-03 1,midg,midg; igrid,midg,midg 2.6512358E-02 3.6131736E-02 gauss-seidel spectral radius is 0.9990744 estimated iterations to convergence 260 setup time was (sec) 0.9800000 now iterating at: 16:27:18 rms-change max change #iterations 8.307703 350.3460 at 10iterations 4.627132 140.4182 at 20iterations 2.547407 67.61337 at 30iterations 1.396826 33.16883 at 40iterations 0.7628232 18.11444 at 50iterations 0.4145098 10.19343 at 60iterations 0.2251384 5.623113 at 70iterations 0.1215400 2.954380 at 80iterations 6.5902002E-02 1.527681 at 90iterations 3.5535712E-02 0.8676624 at 100iterations 1.9149251E-02 0.4794083 at 110iterations 1.0348069E-02 0.2236385 at 120iterations 5.5633695E-03 0.1351700 at 130iterations 2.9885091E-03 7.5475693E-02 at 140iterations 1.6078211E-03 3.7416458E-02 at 150iterations 8.6439162E-04 1.9040108E-02 at 160iterations 4.6511088E-04 1.0417938E-02 at 170iterations 2.4973493E-04 5.4502487E-03 at 180iterations finished qdiffx linear iterations at : 16:27:30 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 2.4973493E-04 5.4502487E-03 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 16:27:31 13.498u 0.246s 0:14.05 97.7% 0+0k 0+0io 0pf+0w