Tue Oct 11 07:14:46 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 07:14:46 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 = 3182 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: 0.5979576 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): 0.6569999 48.87000 ymin,ymax (A): -7.903000 49.36800 zmin,zma (A): 1.442000 60.97800 x,y,z range (A): 48.21300 57.27100 59.53600 scale (grids/A): 0.5979576 object centre (A): 24.76350 20.73250 31.21000 number of atom coordinates read : 3182 total number of charged atoms : 3040 net assigned charge : -0.9999906 assigned positive charge : 479.3919 centred at (gu) : 89.61638 89.22260 90.82272 assigned negative charge : -480.3930 centred at (gu) : 89.54189 89.14079 90.78250 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7555 nv = 96 ne = 84 npr = 64862 no. pairs analyzed = 64862 no. exposed pairs = 3856 no. arc points = 25907 no. surface atoms = 1313 nbur = 1869 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 4379 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3700000 number of dielectric boundary points 3510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2586 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7233498E-09 1.6104219E-09 midg,1,midg; midg,igrid,midg -4.6301052E-09 2.5556661E-09 1,midg,midg; igrid,midg,midg -3.8800216E-09 2.5214735E-09 gauss-seidel spectral radius is 0.9855711 estimated iterations to convergence 68 setup time was (sec) 0.6300000 now iterating at: 07:14:47 rms-change max change #iterations 0.1191479 22.45329 at 10iterations 1.1259131E-02 1.471930 at 20iterations 1.6289277E-03 0.2643967 at 30iterations 4.4008764E-04 8.0207825E-02 at 40iterations 1.3718879E-04 2.5079727E-02 at 50iterations finished qdiffx linear iterations at : 07:14:50 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.3718879E-04 2.5079727E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 07:14:50 3.698u 0.205s 0:04.41 88.2% 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 07:14:50 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 = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.793873 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): 0.6569999 48.87000 ymin,ymax (A): -7.903000 49.36800 zmin,zma (A): 1.442000 60.97800 x,y,z range (A): 48.21300 57.27100 59.53600 scale (grids/A): 1.793873 object centre (A): 24.76350 20.73250 31.21000 number of atom coordinates read : 3182 total number of charged atoms : 3040 net assigned charge : -0.9999906 assigned positive charge : 479.3919 centred at (gu) : 88.84830 87.66722 92.46717 assigned negative charge : -480.3930 centred at (gu) : 88.62551 87.42212 92.34716 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25907 grid for indexing accessible points = 1.400000 m= 30260 mr = 59126 m= 4212 mr = 22873 m= 184 mr = 2618 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 32560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23695 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) : 0.5979576 object centre at (A) : 24.76350 20.73250 31.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0708751E-03 1.4501604E-03 midg,1,midg; midg,igrid,midg -1.9020166E-02 1.1171396E-02 1,midg,midg; igrid,midg,midg -1.5571239E-02 2.5426503E-03 gauss-seidel spectral radius is 0.9985226 estimated iterations to convergence 206 setup time was (sec) 0.9600000 now iterating at: 07:14:51 rms-change max change #iterations 4.222298 187.7761 at 10iterations 1.921773 66.99157 at 20iterations 0.8749335 25.65096 at 30iterations 0.3990390 13.96169 at 40iterations 0.1824346 5.822725 at 50iterations 8.3177619E-02 2.478644 at 60iterations 3.8333785E-02 1.205582 at 70iterations 1.7546400E-02 0.5837135 at 80iterations 8.2144858E-03 0.2635345 at 90iterations 3.9556664E-03 0.1534815 at 100iterations 1.9804873E-03 6.7810059E-02 at 110iterations 1.0440054E-03 4.4284821E-02 at 120iterations finished qdiffx linear iterations at : 07:14:58 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 1.0440054E-03 4.4284821E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 07:14:59 8.103u 0.217s 0:08.83 94.1% 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 07:14:59 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 = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.690809 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): 0.6569999 48.87000 ymin,ymax (A): -7.903000 49.36800 zmin,zma (A): 1.442000 60.97800 x,y,z range (A): 48.21300 57.27100 59.53600 scale (grids/A): 2.690809 object centre (A): 24.76350 20.73250 31.21000 number of atom coordinates read : 3182 total number of charged atoms : 3040 net assigned charge : -0.9999906 assigned positive charge : 479.3919 centred at (gu) : 88.27218 86.50066 93.70062 assigned negative charge : -480.3930 centred at (gu) : 87.93816 86.13314 93.52048 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 191548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25907 grid for indexing accessible points = 1.400000 m= 98786 mr = 143163 m= 34627 mr = 82100 m= 7289 mr = 28275 m= 752 mr = 5439 m= 23 mr = 468 m= 0 mr = 3 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 73577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 24312 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) : 1.793873 object centre at (A) : 24.76350 20.73250 31.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3063450 -0.2528354 midg,1,midg; midg,igrid,midg -0.3917265 0.1335061 1,midg,midg; igrid,midg,midg -0.1810290 7.2554839E-03 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.930000 now iterating at: 07:15:01 rms-change max change #iterations 10.15894 289.9778 at 10iterations 5.898504 124.9273 at 20iterations 3.395753 67.35756 at 30iterations 1.945494 37.36799 at 40iterations 1.117031 24.38439 at 50iterations 0.6392654 11.30966 at 60iterations 0.3651731 6.531162 at 70iterations 0.2086971 4.039130 at 80iterations 0.1191980 2.172867 at 90iterations 6.8173967E-02 1.190712 at 100iterations 3.8808715E-02 0.7120113 at 110iterations 2.2215527E-02 0.3672915 at 120iterations 1.2717730E-02 0.2215042 at 130iterations 7.3060347E-03 0.1319103 at 140iterations 4.2302567E-03 7.7140808E-02 at 150iterations 2.4893400E-03 4.9144745E-02 at 160iterations 1.4908646E-03 2.8017044E-02 at 170iterations 9.2300843E-04 1.8504143E-02 at 180iterations finished qdiffx linear iterations at : 07:15:12 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 9.2300843E-04 1.8504143E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 07:15:13 13.260u 0.221s 0:13.96 96.5% 0+0k 0+0io 0pf+0w