Sat Oct 8 19:00:36 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 Sat Oct 8 2011 at 19:00:37 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6187968 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): -31.67700 17.73100 ymin,ymax (A): -23.73000 23.44100 zmin,zma (A): -13.00100 44.53000 x,y,z range (A): 49.40800 47.17100 57.53100 scale (grids/A): 0.6187968 object centre (A): -6.973000 -0.1444998 15.76450 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 88.44400 89.20525 89.99846 assigned negative charge : -390.0706 centred at (gu) : 88.33894 89.23476 89.89077 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6683 nv = 96 ne = 84 npr = 53133 no. pairs analyzed = 53133 no. exposed pairs = 3043 no. arc points = 21877 no. surface atoms = 1034 nbur = 1568 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3731 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3500000 number of dielectric boundary points 3239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2179 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4190653E-09 1.0427373E-08 midg,1,midg; midg,igrid,midg 6.5215566E-09 1.4387319E-09 1,midg,midg; igrid,midg,midg -4.7146025E-09 7.3036475E-09 gauss-seidel spectral radius is 0.9864764 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 19:00:37 rms-change max change #iterations 0.1303638 18.50819 at 10iterations 1.1647255E-02 1.959194 at 20iterations 1.0976222E-03 0.1476555 at 30iterations 1.0255009E-04 1.5371323E-02 at 40iterations 9.5179275E-06 1.5563965E-03 at 50iterations finished qdiffx linear iterations at : 19:00:41 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 9.5179275E-06 1.5563965E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 19:00:41 4.199u 0.281s 0:04.83 92.5% 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 8 2011 at 19:00:41 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.856390 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): -31.67700 17.73100 ymin,ymax (A): -23.73000 23.44100 zmin,zma (A): -13.00100 44.53000 x,y,z range (A): 49.40800 47.17100 57.53100 scale (grids/A): 1.856390 object centre (A): -6.973000 -0.1444998 15.76450 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 85.33152 87.61529 89.99483 assigned negative charge : -390.0706 centred at (gu) : 85.01679 87.70383 89.67222 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21877 grid for indexing accessible points = 1.400000 m= 26314 mr = 50465 m= 4103 mr = 19771 m= 252 mr = 2652 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3751 time to turn everything in is 0.6400000 number of dielectric boundary points 29791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19290 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) : 0.6187968 object centre at (A) : -6.973000 -0.1444998 15.76450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8253261E-02 2.6629677E-02 midg,1,midg; midg,igrid,midg 1.3575313E-02 3.3919038E-03 1,midg,midg; igrid,midg,midg -3.7397153E-03 3.4751400E-02 gauss-seidel spectral radius is 0.9985664 estimated iterations to convergence 209 setup time was (sec) 0.9400000 now iterating at: 19:00:43 rms-change max change #iterations 4.051740 170.4290 at 10iterations 1.852406 70.57027 at 20iterations 0.8530978 31.04613 at 30iterations 0.3921709 13.25594 at 40iterations 0.1799882 6.289345 at 50iterations 8.2701705E-02 2.718258 at 60iterations 3.8184509E-02 1.233965 at 70iterations 1.7556148E-02 0.5410805 at 80iterations 8.0626570E-03 0.2656059 at 90iterations 3.7063267E-03 0.1157274 at 100iterations 1.6992071E-03 6.0836792E-02 at 110iterations 7.8517542E-04 2.4547577E-02 at 120iterations finished qdiffx linear iterations at : 19:00:51 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 7.8517542E-04 2.4547577E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 19:00:52 9.669u 0.336s 0:10.29 97.0% 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 Sat Oct 8 2011 at 19:00:52 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.784586 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): -31.67700 17.73100 ymin,ymax (A): -23.73000 23.44100 zmin,zma (A): -13.00100 44.53000 x,y,z range (A): 49.40800 47.17100 57.53100 scale (grids/A): 2.784586 object centre (A): -6.973000 -0.1444998 15.76450 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 82.99713 86.42276 89.99213 assigned negative charge : -390.0706 centred at (gu) : 82.52508 86.55566 89.50825 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21877 grid for indexing accessible points = 1.400000 m= 85479 mr = 121742 m= 30768 mr = 70850 m= 7415 mr = 24960 m= 1200 mr = 5734 m= 62 mr = 862 m= 0 mr = 23 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 12794 time to turn everything in is 1.650000 number of dielectric boundary points 67073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 19694 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) : 1.856390 object centre at (A) : -6.973000 -0.1444998 15.76450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1493790 0.3948257 midg,1,midg; midg,igrid,midg 0.1632387 3.7681721E-02 1,midg,midg; igrid,midg,midg -1.0114777E-02 0.4322342 gauss-seidel spectral radius is 0.9992355 estimated iterations to convergence 285 setup time was (sec) 1.990000 now iterating at: 19:00:54 rms-change max change #iterations 9.545332 368.1274 at 10iterations 5.479492 123.2291 at 20iterations 3.138178 65.91669 at 30iterations 1.791831 33.27406 at 40iterations 1.022210 19.10489 at 50iterations 0.5821172 11.60908 at 60iterations 0.3320354 6.903212 at 70iterations 0.1888850 3.567204 at 80iterations 0.1075362 2.043649 at 90iterations 6.1202586E-02 1.285042 at 100iterations 3.4849834E-02 0.6407747 at 110iterations 1.9788148E-02 0.3590298 at 120iterations 1.1249484E-02 0.2033157 at 130iterations 6.4122779E-03 0.1306400 at 140iterations 3.6497428E-03 6.5581322E-02 at 150iterations 2.0729194E-03 3.9974213E-02 at 160iterations 1.1822230E-03 2.2459984E-02 at 170iterations 6.7281496E-04 1.2397766E-02 at 180iterations finished qdiffx linear iterations at : 19:01:08 total time elapsed so far: 16.04000 # loops : 180 mean,max change (kT/e) : 6.7281496E-04 1.2397766E-02 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.22000 DelPhi exited at 19:01:09 16.218u 0.329s 0:16.85 98.1% 0+0k 0+0io 0pf+0w