Tue Oct 11 03:45:45 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 Tue Oct 11 2011 at 03:45:45 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIR 69 has a net charge of 0.5140 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: 0.6607153 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): 36.97400 85.66199 ymin,ymax (A): -4.833000 49.04800 zmin,zma (A): -15.73500 33.91400 x,y,z range (A): 48.68799 53.88100 49.64900 scale (grids/A): 0.6607153 object centre (A): 61.31800 22.10750 9.089499 number of atom coordinates read : 2762 total number of charged atoms : 2615 net assigned charge : 5.514015 assigned positive charge : 423.1258 centred at (gu) : 88.64140 90.59331 90.58370 assigned negative charge : -417.6122 centred at (gu) : 88.81760 90.34734 90.59888 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8054 nv = 96 ne = 84 npr = 56532 no. pairs analyzed = 56532 no. exposed pairs = 3279 no. arc points = 22693 no. surface atoms = 1102 nbur = 1660 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4645 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.3600000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2250 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4877788E-08 1.1392518E-08 midg,1,midg; midg,igrid,midg -3.6260797E-08 7.4018352E-08 1,midg,midg; igrid,midg,midg 6.7748438E-08 -1.8917172E-08 gauss-seidel spectral radius is 0.9881378 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:45:46 rms-change max change #iterations 0.1812016 27.62435 at 10iterations 1.9443000E-02 2.698029 at 20iterations 2.1741462E-03 0.3131866 at 30iterations 2.5175262E-04 3.3031464E-02 at 40iterations 3.5857200E-05 5.7678223E-03 at 50iterations finished qdiffx linear iterations at : 03:45:50 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 3.5857200E-05 5.7678223E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 03:45:50 4.175u 0.281s 0:05.06 87.9% 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 Tue Oct 11 2011 at 03:45:50 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIR 69 has a net charge of 0.5140 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: 1.982146 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): 36.97400 85.66199 ymin,ymax (A): -4.833000 49.04800 zmin,zma (A): -15.73500 33.91400 x,y,z range (A): 48.68799 53.88100 49.64900 scale (grids/A): 1.982146 object centre (A): 61.31800 22.10750 9.089499 number of atom coordinates read : 2762 total number of charged atoms : 2615 net assigned charge : 5.514015 assigned positive charge : 423.1258 centred at (gu) : 85.92393 91.77924 91.75082 assigned negative charge : -417.6122 centred at (gu) : 86.45256 91.04160 91.79663 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22693 grid for indexing accessible points = 1.400000 m= 33515 mr = 60977 m= 5912 mr = 25539 m= 351 mr = 3921 m= 3 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.7700000 number of dielectric boundary points 35106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20654 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) : 0.6607153 object centre at (A) : 61.31800 22.10750 9.089499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3565096E-03 -3.5834783E-03 midg,1,midg; midg,igrid,midg -6.1592959E-02 5.9840258E-02 1,midg,midg; igrid,midg,midg 0.1122200 -2.9663842E-03 gauss-seidel spectral radius is 0.9987476 estimated iterations to convergence 224 setup time was (sec) 1.070000 now iterating at: 03:45:52 rms-change max change #iterations 4.856643 188.1616 at 10iterations 2.359780 75.63170 at 20iterations 1.143213 33.67657 at 30iterations 0.5555431 16.24694 at 40iterations 0.2693633 7.967617 at 50iterations 0.1306563 3.816144 at 60iterations 6.3234597E-02 1.844886 at 70iterations 3.0767590E-02 0.9239540 at 80iterations 1.4875112E-02 0.3962803 at 90iterations 7.2396556E-03 0.2237015 at 100iterations 3.4974588E-03 0.1002550 at 110iterations 1.7010071E-03 5.7193756E-02 at 120iterations finished qdiffx linear iterations at : 03:46:00 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 1.7010071E-03 5.7193756E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 03:46:01 9.816u 0.300s 0:10.78 93.7% 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 Tue Oct 11 2011 at 03:46:01 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIR 69 has a net charge of 0.5140 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: 2.973219 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): 36.97400 85.66199 ymin,ymax (A): -4.833000 49.04800 zmin,zma (A): -15.73500 33.91400 x,y,z range (A): 48.68799 53.88100 49.64900 scale (grids/A): 2.973219 object centre (A): 61.31800 22.10750 9.089499 number of atom coordinates read : 2762 total number of charged atoms : 2615 net assigned charge : 5.514015 assigned positive charge : 423.1258 centred at (gu) : 83.88548 92.66885 92.62618 assigned negative charge : -417.6122 centred at (gu) : 84.67882 91.56245 92.69487 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 198069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22693 grid for indexing accessible points = 1.400000 m= 106014 mr = 146807 m= 41694 mr = 88315 m= 10842 mr = 34361 m= 1695 mr = 8457 m= 86 mr = 1183 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 2232 time to turn everything in is 2.010000 number of dielectric boundary points 79232 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 20920 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) : 1.982146 object centre at (A) : 61.31800 22.10750 9.089499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3675521E-02 -4.9996272E-02 midg,1,midg; midg,igrid,midg -0.5939855 0.1629200 1,midg,midg; igrid,midg,midg 1.142115 -5.3305659E-02 gauss-seidel spectral radius is 0.9992883 estimated iterations to convergence 296 setup time was (sec) 2.330000 now iterating at: 03:46:04 rms-change max change #iterations 11.01964 373.5985 at 10iterations 6.509764 174.0455 at 20iterations 3.836774 76.49792 at 30iterations 2.259369 44.06639 at 40iterations 1.324716 24.68618 at 50iterations 0.7752181 14.20770 at 60iterations 0.4539909 8.003325 at 70iterations 0.2652208 4.728519 at 80iterations 0.1548409 3.021187 at 90iterations 9.0395071E-02 1.473175 at 100iterations 5.2727886E-02 0.9173474 at 110iterations 3.0790770E-02 0.5272865 at 120iterations 1.7904626E-02 0.2917805 at 130iterations 1.0497777E-02 0.1953125 at 140iterations 6.1633382E-03 0.1013718 at 150iterations 3.6282854E-03 5.7991028E-02 at 160iterations 2.1602768E-03 4.1787148E-02 at 170iterations 1.3070663E-03 2.2163391E-02 at 180iterations finished qdiffx linear iterations at : 03:46:18 total time elapsed so far: 16.59000 # loops : 180 mean,max change (kT/e) : 1.3070663E-03 2.2163391E-02 energy calculations done at 16.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.77000 DelPhi exited at 03:46:19 16.768u 0.332s 0:17.91 95.4% 0+0k 0+0io 0pf+0w