Tue Oct 11 06:32:46 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 Tue Oct 11 2011 at 06:32:46 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 = 2064 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: 0.7222853 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): -3.0000210E-03 40.88500 ymin,ymax (A): -18.29000 26.17700 zmin,zma (A): -14.94800 34.34000 x,y,z range (A): 40.88800 44.46700 49.28800 scale (grids/A): 0.7222853 object centre (A): 20.44100 3.943501 9.696000 number of atom coordinates read : 2064 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 89.07267 90.19846 89.20271 assigned negative charge : -307.4362 centred at (gu) : 89.02040 90.07278 89.12160 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7341 nv = 96 ne = 84 npr = 41761 no. pairs analyzed = 41761 no. exposed pairs = 2441 no. arc points = 16810 no. surface atoms = 832 nbur = 1232 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4275 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1565 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6032234E-08 1.1375617E-07 midg,1,midg; midg,igrid,midg -7.1539970E-09 1.6779607E-07 1,midg,midg; igrid,midg,midg 5.0183051E-08 9.5029229E-08 gauss-seidel spectral radius is 0.9900010 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 06:32:47 rms-change max change #iterations 0.2188693 27.10617 at 10iterations 2.8679078E-02 4.152279 at 20iterations 3.8650313E-03 0.5089874 at 30iterations 6.0219603E-04 8.4625244E-02 at 40iterations 1.2917006E-04 1.5407562E-02 at 50iterations finished qdiffx linear iterations at : 06:32:49 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.2917006E-04 1.5407562E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 06:32:50 3.428u 0.181s 0:04.02 89.5% 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 Tue Oct 11 2011 at 06:32:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 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: 2.166856 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): -3.0000210E-03 40.88500 ymin,ymax (A): -18.29000 26.17700 zmin,zma (A): -14.94800 34.34000 x,y,z range (A): 40.88800 44.46700 49.28800 scale (grids/A): 2.166856 object centre (A): 20.44100 3.943501 9.696000 number of atom coordinates read : 2064 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 87.21804 90.59541 87.60796 assigned negative charge : -307.4362 centred at (gu) : 87.06139 90.21869 87.36491 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16810 grid for indexing accessible points = 1.400000 m= 31424 mr = 55676 m= 6335 mr = 24079 m= 631 mr = 4363 m= 13 mr = 344 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15394 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) : 0.7222853 object centre at (A) : 20.44100 3.943501 9.696000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6878159E-02 4.6849821E-02 midg,1,midg; midg,igrid,midg 1.2992086E-02 5.5396199E-02 1,midg,midg; igrid,midg,midg 3.1509902E-02 1.7967047E-02 gauss-seidel spectral radius is 0.9988684 estimated iterations to convergence 235 setup time was (sec) 0.9000000 now iterating at: 06:32:51 rms-change max change #iterations 4.745470 207.5355 at 10iterations 2.380977 81.11440 at 20iterations 1.201280 41.38920 at 30iterations 0.6057041 18.56601 at 40iterations 0.3034458 8.646085 at 50iterations 0.1525743 5.272594 at 60iterations 7.6847062E-02 2.297731 at 70iterations 3.8659696E-02 1.161758 at 80iterations 1.9491443E-02 0.5376358 at 90iterations 9.8776985E-03 0.2986908 at 100iterations 4.9733808E-03 0.1411896 at 110iterations 2.5597471E-03 7.8231812E-02 at 120iterations finished qdiffx linear iterations at : 06:32:58 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.5597471E-03 7.8231812E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 06:32:59 7.975u 0.215s 0:08.76 93.3% 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 06:32:59 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 = 2064 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: 3.250284 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): -3.0000210E-03 40.88500 ymin,ymax (A): -18.29000 26.17700 zmin,zma (A): -14.94800 34.34000 x,y,z range (A): 40.88800 44.46700 49.28800 scale (grids/A): 3.250284 object centre (A): 20.44100 3.943501 9.696000 number of atom coordinates read : 2064 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 85.82703 90.89315 86.41199 assigned negative charge : -307.4362 centred at (gu) : 85.59200 90.32807 86.04744 start vw surface at 0.1500000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 178529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16810 grid for indexing accessible points = 1.400000 m= 97692 mr = 133586 m= 40320 mr = 81749 m= 12233 mr = 33558 m= 2758 mr = 9654 m= 361 mr = 2103 m= 15 mr = 261 m= 0 mr = 3 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 70994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 15488 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) : 2.166856 object centre at (A) : 20.44100 3.943501 9.696000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2254075 0.1805380 midg,1,midg; midg,igrid,midg 9.8981880E-02 0.4417768 1,midg,midg; igrid,midg,midg 0.2939536 9.8557577E-02 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 2.280000 now iterating at: 06:33:01 rms-change max change #iterations 10.43801 366.8531 at 10iterations 6.207534 143.8310 at 20iterations 3.687300 75.20027 at 30iterations 2.186155 50.66684 at 40iterations 1.290977 23.88866 at 50iterations 0.7614269 14.97711 at 60iterations 0.4489625 8.110683 at 70iterations 0.2644477 5.049541 at 80iterations 0.1557096 2.719589 at 90iterations 9.1879539E-02 1.636944 at 100iterations 5.4033812E-02 1.015253 at 110iterations 3.1938251E-02 0.5710347 at 120iterations 1.9001793E-02 0.3408508 at 130iterations 1.1401390E-02 0.2130456 at 140iterations 6.9888067E-03 0.1172733 at 150iterations 4.4358522E-03 8.5998535E-02 at 160iterations 2.9373548E-03 5.9795380E-02 at 170iterations 2.0628558E-03 3.5507202E-02 at 180iterations finished qdiffx linear iterations at : 06:33:12 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 2.0628558E-03 3.5507202E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 06:33:12 13.039u 0.256s 0:13.61 97.5% 0+0k 0+0io 0pf+0w