Sat Oct 8 18:22:59 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 18:22:59 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 = 3287 !!! WARNING: ILE 378 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5492302 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): -13.59800 42.06100 ymin,ymax (A): -72.67000 -7.852000 zmin,zma (A): -21.87700 24.95900 x,y,z range (A): 55.65900 64.81800 46.83600 scale (grids/A): 0.5492302 object centre (A): 14.23150 -40.26100 1.540999 number of atom coordinates read : 3287 total number of charged atoms : 3142 net assigned charge : -4.771982 assigned positive charge : 488.1908 centred at (gu) : 90.45255 90.41421 90.06456 assigned negative charge : -492.9639 centred at (gu) : 90.49727 90.40686 90.04855 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6572 nv = 96 ne = 84 npr = 65774 no. pairs analyzed = 65774 no. exposed pairs = 4116 no. arc points = 28310 no. surface atoms = 1394 nbur = 1893 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 264 mr = 3518 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2913 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6197773E-10 -2.0585610E-10 midg,1,midg; midg,igrid,midg -3.5937917E-10 -3.0298977E-10 1,midg,midg; igrid,midg,midg 2.8990043E-11 -7.9341639E-10 gauss-seidel spectral radius is 0.9829301 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 18:23:00 rms-change max change #iterations 8.0403522E-02 12.71948 at 10iterations 5.5483333E-03 0.8646927 at 20iterations 4.0096400E-04 6.2009096E-02 at 30iterations 4.3845183E-05 7.2243065E-03 at 40iterations 8.8564411E-06 1.7656088E-03 at 50iterations finished qdiffx linear iterations at : 18:23:04 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 8.8564411E-06 1.7656088E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 18:23:04 4.295u 0.278s 0:04.96 91.9% 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 18:23:04 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 = 3287 !!! WARNING: ILE 378 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.647690 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): -13.59800 42.06100 ymin,ymax (A): -72.67000 -7.852000 zmin,zma (A): -21.87700 24.95900 x,y,z range (A): 55.65900 64.81800 46.83600 scale (grids/A): 1.647690 object centre (A): 14.23150 -40.26100 1.540999 number of atom coordinates read : 3287 total number of charged atoms : 3142 net assigned charge : -4.771982 assigned positive charge : 488.1908 centred at (gu) : 91.35648 91.24209 90.19319 assigned negative charge : -492.9639 centred at (gu) : 91.49171 91.21986 90.14522 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28310 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24007 mr = 50549 m= 2566 mr = 16977 m= 79 mr = 1297 m= 0 mr = 19 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.6500000 number of dielectric boundary points 30422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 24118 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) : 0.5492302 object centre at (A) : 14.23150 -40.26100 1.540999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9269204E-03 -3.9109648E-03 midg,1,midg; midg,igrid,midg 6.6033481E-03 1.8603444E-02 1,midg,midg; igrid,midg,midg -1.1994933E-02 -7.6920358E-03 gauss-seidel spectral radius is 0.9982517 estimated iterations to convergence 190 setup time was (sec) 0.9300000 now iterating at: 18:23:06 rms-change max change #iterations 3.582484 159.8610 at 10iterations 1.505858 53.59176 at 20iterations 0.6407095 22.54554 at 30iterations 0.2719037 8.874078 at 40iterations 0.1152767 4.222637 at 50iterations 4.8858982E-02 1.684435 at 60iterations 2.0672271E-02 0.7125044 at 70iterations 8.7988051E-03 0.2951288 at 80iterations 3.7391521E-03 0.1270933 at 90iterations 1.5945499E-03 5.7720184E-02 at 100iterations 6.8049069E-04 2.3695827E-02 at 110iterations 2.9334260E-04 1.0665894E-02 at 120iterations finished qdiffx linear iterations at : 18:23:14 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 2.9334260E-04 1.0665894E-02 energy calculations done at 9.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 18:23:15 9.786u 0.371s 0:10.42 97.4% 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 18:23:15 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 = 3287 !!! WARNING: ILE 378 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.471536 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): -13.59800 42.06100 ymin,ymax (A): -72.67000 -7.852000 zmin,zma (A): -21.87700 24.95900 x,y,z range (A): 55.65900 64.81800 46.83600 scale (grids/A): 2.471536 object centre (A): 14.23150 -40.26100 1.540999 number of atom coordinates read : 3287 total number of charged atoms : 3142 net assigned charge : -4.771982 assigned positive charge : 488.1908 centred at (gu) : 92.03462 91.86275 90.28957 assigned negative charge : -492.9639 centred at (gu) : 92.23733 91.82970 90.21765 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 168648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28310 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81818 mr = 123358 m= 24522 mr = 65717 m= 4137 mr = 18769 m= 358 mr = 2711 m= 6 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 1.640000 number of dielectric boundary points 68744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 25111 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) : 1.647690 object centre at (A) : 14.23150 -40.26100 1.540999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9089671E-02 -3.3421829E-02 midg,1,midg; midg,igrid,midg 0.2260693 0.5328441 1,midg,midg; igrid,midg,midg -0.2037863 -7.9903245E-02 gauss-seidel spectral radius is 0.9991642 estimated iterations to convergence 273 setup time was (sec) 1.990000 now iterating at: 18:23:17 rms-change max change #iterations 9.162121 307.4979 at 10iterations 5.184149 117.6735 at 20iterations 2.919425 63.68383 at 30iterations 1.639222 34.49339 at 40iterations 0.9181879 17.51735 at 50iterations 0.5112245 10.89483 at 60iterations 0.2852893 5.763203 at 70iterations 0.1587822 3.167538 at 80iterations 8.8384688E-02 1.660591 at 90iterations 4.9153693E-02 0.9299994 at 100iterations 2.7273020E-02 0.5173053 at 110iterations 1.5196684E-02 0.2950623 at 120iterations 8.4118256E-03 0.1805067 at 130iterations 4.7002910E-03 0.1101990 at 140iterations 2.6083507E-03 4.6499252E-02 at 150iterations 1.4495165E-03 2.8285027E-02 at 160iterations 8.1056281E-04 1.6147614E-02 at 170iterations 4.5422843E-04 9.5338821E-03 at 180iterations finished qdiffx linear iterations at : 18:23:32 total time elapsed so far: 16.37000 # loops : 180 mean,max change (kT/e) : 4.5422843E-04 9.5338821E-03 energy calculations done at 16.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.56000 DelPhi exited at 18:23:32 16.563u 0.316s 0:17.41 96.8% 0+0k 0+0io 0pf+0w