Sat Oct 8 11:35:22 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 8 2011 at 11:35:22 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 0.6209555 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): -60.81500 -14.21300 ymin,ymax (A): -75.70500 -23.57800 zmin,zma (A): -32.56500 24.76600 x,y,z range (A): 46.60200 52.12700 57.33100 scale (grids/A): 0.6209555 object centre (A): -37.51400 -49.64150 -3.899501 number of atom coordinates read : 2581 total number of charged atoms : 2421 net assigned charge : -0.9999937 assigned positive charge : 376.1128 centred at (gu) : 89.90813 92.22105 91.36527 assigned negative charge : -377.1134 centred at (gu) : 89.85848 92.18211 91.29286 start vw surface at 0.3000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 6720 nv = 96 ne = 84 npr = 52636 no. pairs analyzed = 52636 no. exposed pairs = 3335 no. arc points = 23194 no. surface atoms = 1130 nbur = 1451 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3558 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 3456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2295 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 8083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2655244E-09 5.1661453E-09 midg,1,midg; midg,igrid,midg -2.1736448E-09 2.6905902E-09 1,midg,midg; igrid,midg,midg -4.3318322E-09 2.2530764E-09 gauss-seidel spectral radius is 0.9865716 estimated iterations to convergence 71 setup time was (sec) 0.8300000 now iterating at: 11:35:23 rms-change max change #iterations 0.1237661 21.00470 at 10iterations 1.1281727E-02 1.716850 at 20iterations 1.0456023E-03 0.1470060 at 30iterations 1.0499154E-04 1.7148972E-02 at 40iterations 1.2882569E-05 1.9626617E-03 at 50iterations finished qdiffx linear iterations at : 11:35:27 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 1.2882569E-05 1.9626617E-03 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 11:35:27 4.719u 0.420s 0:05.61 91.4% 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 Sat Oct 8 2011 at 11:35:27 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 1.862867 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): -60.81500 -14.21300 ymin,ymax (A): -75.70500 -23.57800 zmin,zma (A): -32.56500 24.76600 x,y,z range (A): 46.60200 52.12700 57.33100 scale (grids/A): 1.862867 object centre (A): -37.51400 -49.64150 -3.899501 number of atom coordinates read : 2581 total number of charged atoms : 2421 net assigned charge : -0.9999937 assigned positive charge : 376.1128 centred at (gu) : 89.72407 96.66240 94.09516 assigned negative charge : -377.1134 centred at (gu) : 89.57504 96.54614 93.87857 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23194 grid for indexing accessible points = 1.400000 m= 25090 mr = 49398 m= 3391 mr = 17919 m= 132 mr = 1923 m= 1 mr = 35 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 0.5900000 number of dielectric boundary points 31817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19000 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) : 0.6209555 object centre at (A) : -37.51400 -49.64150 -3.899501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3932016E-02 4.6937309E-02 midg,1,midg; midg,igrid,midg -9.2037944E-03 1.0153783E-02 1,midg,midg; igrid,midg,midg -5.6218477E-03 -8.9126471E-03 gauss-seidel spectral radius is 0.9985703 estimated iterations to convergence 210 setup time was (sec) 0.8900000 now iterating at: 11:35:29 rms-change max change #iterations 3.977437 179.6762 at 10iterations 1.824914 62.36493 at 20iterations 0.8400607 28.33459 at 30iterations 0.3864011 13.29434 at 40iterations 0.1775063 5.790302 at 50iterations 8.1719480E-02 2.686056 at 60iterations 3.7524316E-02 1.172951 at 70iterations 1.7270939E-02 0.6257620 at 80iterations 7.9564648E-03 0.2497496 at 90iterations 3.6690303E-03 0.1150143 at 100iterations 1.6875596E-03 5.7289124E-02 at 110iterations 7.7656761E-04 2.5734901E-02 at 120iterations finished qdiffx linear iterations at : 11:35:38 total time elapsed so far: 10.46000 # loops : 120 mean,max change (kT/e) : 7.7656761E-04 2.5734901E-02 energy calculations done at 10.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 11:35:39 10.632u 0.451s 0:11.43 96.9% 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 Sat Oct 8 2011 at 11:35:39 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 2.794300 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): -60.81500 -14.21300 ymin,ymax (A): -75.70500 -23.57800 zmin,zma (A): -32.56500 24.76600 x,y,z range (A): 46.60200 52.12700 57.33100 scale (grids/A): 2.794300 object centre (A): -37.51400 -49.64150 -3.899501 number of atom coordinates read : 2581 total number of charged atoms : 2421 net assigned charge : -0.9999937 assigned positive charge : 376.1128 centred at (gu) : 89.58593 99.99358 96.14267 assigned negative charge : -377.1134 centred at (gu) : 89.36246 99.81914 95.81780 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 167735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23194 grid for indexing accessible points = 1.400000 m= 82236 mr = 120174 m= 28064 mr = 66242 m= 5918 mr = 21998 m= 689 mr = 4181 m= 38 mr = 378 m= 0 mr = 19 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 71688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 19368 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) : 1.862867 object centre at (A) : -37.51400 -49.64150 -3.899501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2201203 0.9322067 midg,1,midg; midg,igrid,midg -5.7103839E-02 0.2169080 1,midg,midg; igrid,midg,midg -3.1803627E-02 -0.1221216 gauss-seidel spectral radius is 0.9992454 estimated iterations to convergence 287 setup time was (sec) 1.820000 now iterating at: 11:35:41 rms-change max change #iterations 9.532754 324.4259 at 10iterations 5.577760 138.7484 at 20iterations 3.234406 64.21619 at 30iterations 1.870089 36.38551 at 40iterations 1.078784 21.98907 at 50iterations 0.6196894 12.60439 at 60iterations 0.3557147 6.813189 at 70iterations 0.2043028 4.003757 at 80iterations 0.1172707 2.453171 at 90iterations 6.7013651E-02 1.300832 at 100iterations 3.8453955E-02 0.7119961 at 110iterations 2.2021940E-02 0.4350815 at 120iterations 1.2579502E-02 0.2776051 at 130iterations 7.2161197E-03 0.1368775 at 140iterations 4.1273106E-03 7.8387499E-02 at 150iterations 2.3669051E-03 4.3753147E-02 at 160iterations 1.3611709E-03 2.4930954E-02 at 170iterations 7.8394933E-04 1.4941350E-02 at 180iterations finished qdiffx linear iterations at : 11:35:57 total time elapsed so far: 17.82000 # loops : 180 mean,max change (kT/e) : 7.8394933E-04 1.4941350E-02 energy calculations done at 17.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 11:35:58 17.994u 0.490s 0:19.09 96.8% 0+0k 0+0io 0pf+0w