Sat Oct 15 14:49:23 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 14:49:23 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7474595 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): 34.69100 82.31900 ymin,ymax (A): 11.20100 52.59000 zmin,zma (A): 25.65700 60.60500 x,y,z range (A): 47.62800 41.38900 34.94801 scale (grids/A): 0.7474595 object centre (A): 58.50500 31.89550 43.13100 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 90.41351 90.33345 88.59472 assigned negative charge : -192.8082 centred at (gu) : 90.55503 90.25664 88.54974 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4863 nv = 96 ne = 84 npr = 27562 no. pairs analyzed = 27562 no. exposed pairs = 1622 no. arc points = 12070 no. surface atoms = 555 nbur = 806 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 2528 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2000000 number of dielectric boundary points 2607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1100 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8450813E-07 2.8269358E-07 midg,1,midg; midg,igrid,midg 2.6055974E-07 4.0926443E-07 1,midg,midg; igrid,midg,midg 3.9937811E-07 2.4643199E-07 gauss-seidel spectral radius is 0.9905868 estimated iterations to convergence 84 setup time was (sec) 0.4200000 now iterating at: 14:49:23 rms-change max change #iterations 0.1995731 33.04373 at 10iterations 2.7003590E-02 5.445816 at 20iterations 3.6351385E-03 0.5886250 at 30iterations 4.9499859E-04 0.1061821 at 40iterations 6.6668799E-05 1.1054993E-02 at 50iterations finished qdiffx linear iterations at : 14:49:26 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 6.6668799E-05 1.1054993E-02 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 14:49:26 3.034u 0.147s 0:03.49 90.8% 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 14:49:26 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.242378 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): 34.69100 82.31900 ymin,ymax (A): 11.20100 52.59000 zmin,zma (A): 25.65700 60.60500 x,y,z range (A): 47.62800 41.38900 34.94801 scale (grids/A): 2.242378 object centre (A): 58.50500 31.89550 43.13100 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 91.24073 91.00036 85.78418 assigned negative charge : -192.8082 centred at (gu) : 91.66531 90.77015 85.64940 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 50886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12070 grid for indexing accessible points = 1.400000 m= 18805 mr = 33678 m= 4214 mr = 13865 m= 552 mr = 2897 m= 24 mr = 357 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 469 time to turn everything in is 0.4000000 number of dielectric boundary points 23677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9857 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) : 0.7474595 object centre at (A) : 58.50500 31.89550 43.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1600754E-02 3.0402178E-02 midg,1,midg; midg,igrid,midg 2.9013254E-02 8.6782679E-02 1,midg,midg; igrid,midg,midg 0.1305431 0.1059044 gauss-seidel spectral radius is 0.9988628 estimated iterations to convergence 235 setup time was (sec) 0.6600000 now iterating at: 14:49:27 rms-change max change #iterations 3.897612 182.8711 at 10iterations 1.941485 76.37784 at 20iterations 0.9680890 33.54701 at 30iterations 0.4831977 17.24064 at 40iterations 0.2413985 8.879684 at 50iterations 0.1211173 4.484196 at 60iterations 6.0128678E-02 2.235566 at 70iterations 3.0122548E-02 1.203704 at 80iterations 1.4987930E-02 0.5250340 at 90iterations 7.5025088E-03 0.2644753 at 100iterations 3.7440865E-03 0.1288071 at 110iterations 1.8648829E-03 6.7611694E-02 at 120iterations finished qdiffx linear iterations at : 14:49:33 total time elapsed so far: 6.560000 # loops : 120 mean,max change (kT/e) : 1.8648829E-03 6.7611694E-02 energy calculations done at 6.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.720000 DelPhi exited at 14:49:34 6.727u 0.181s 0:07.22 95.5% 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 15 2011 at 14:49:34 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.363568 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): 34.69100 82.31900 ymin,ymax (A): 11.20100 52.59000 zmin,zma (A): 25.65700 60.60500 x,y,z range (A): 47.62800 41.38900 34.94801 scale (grids/A): 3.363568 object centre (A): 58.50500 31.89550 43.13100 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 91.86113 91.50054 83.67630 assigned negative charge : -192.8082 centred at (gu) : 92.49797 91.15523 83.47417 start vw surface at 0.1300000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 117217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12070 grid for indexing accessible points = 1.400000 m= 58339 mr = 81379 m= 24224 mr = 47446 m= 8248 mr = 19742 m= 2091 mr = 6489 m= 356 mr = 1630 m= 20 mr = 266 m= 0 mr = 13 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1639 time to turn everything in is 1.220000 number of dielectric boundary points 53530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 9904 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) : 2.242378 object centre at (A) : 58.50500 31.89550 43.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3453853 0.1641970 midg,1,midg; midg,igrid,midg 0.1435531 0.7276692 1,midg,midg; igrid,midg,midg 1.041210 0.8086774 gauss-seidel spectral radius is 0.9992984 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 14:49:35 rms-change max change #iterations 8.529561 239.0219 at 10iterations 4.974771 114.3422 at 20iterations 2.899764 63.29841 at 30iterations 1.692180 34.05613 at 40iterations 0.9849241 21.80014 at 50iterations 0.5724175 10.99901 at 60iterations 0.3333062 6.903400 at 70iterations 0.1936750 3.792086 at 80iterations 0.1127056 2.434118 at 90iterations 6.5602913E-02 1.363074 at 100iterations 3.8227160E-02 0.7948194 at 110iterations 2.2199830E-02 0.4470978 at 120iterations 1.2938683E-02 0.2535820 at 130iterations 7.5214589E-03 0.1473169 at 140iterations 4.3841400E-03 9.1307640E-02 at 150iterations 2.5437216E-03 4.9586415E-02 at 160iterations 1.4824892E-03 3.0364990E-02 at 170iterations 8.6014770E-04 1.8562317E-02 at 180iterations finished qdiffx linear iterations at : 14:49:45 total time elapsed so far: 10.76000 # loops : 180 mean,max change (kT/e) : 8.6014770E-04 1.8562317E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.93000 DelPhi exited at 14:49:45 10.934u 0.175s 0:11.50 96.5% 0+0k 0+0io 0pf+0w