Wed Dec 21 14:21:28 PST 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+sph2.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 = amb2.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 Wed Dec 21 2011 at 14:21:29 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5957760 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): -34.76100 10.13200 ymin,ymax (A): 0.5979999 41.31000 zmin,zma (A): -2.774000 56.98000 x,y,z range (A): 44.89300 40.71200 59.75400 scale (grids/A): 0.5957760 object centre (A): -12.31450 20.95400 27.10300 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 267.6024 centred at (gu) : 90.27362 89.69105 90.48298 assigned negative charge : -289.5542 centred at (gu) : 90.17856 89.83421 90.49879 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4717 nv = 96 ne = 84 npr = 40119 no. pairs analyzed = 40119 no. exposed pairs = 2462 no. arc points = 17142 no. surface atoms = 841 nbur = 1117 mkacc time = 6.9999993E-02 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 = 1.456000 m= 226 mr = 2544 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1704 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 5643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0371104E-09 -9.5520205E-09 midg,1,midg; midg,igrid,midg -5.1700608E-09 -1.0896268E-08 1,midg,midg; igrid,midg,midg -9.8748494E-09 -6.3217391E-09 gauss-seidel spectral radius is 0.9853671 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 14:21:30 rms-change max change #iterations 9.4659723E-02 18.38918 at 10iterations 7.8649027E-03 1.496914 at 20iterations 6.6097436E-04 0.1244812 at 30iterations 5.4802840E-05 9.7284317E-03 at 40iterations 4.4404214E-06 8.2206726E-04 at 50iterations finished qdiffx linear iterations at : 14:21:33 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 4.4404214E-06 8.2206726E-04 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 14:21:44 3.725u 0.295s 0:15.43 25.9% 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 Wed Dec 21 2011 at 14:21:44 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.787328 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): -34.76100 10.13200 ymin,ymax (A): 0.5979999 41.31000 zmin,zma (A): -2.774000 56.98000 x,y,z range (A): 44.89300 40.71200 59.75400 scale (grids/A): 1.787328 object centre (A): -12.31450 20.95400 27.10300 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 267.6024 centred at (gu) : 90.82104 89.07343 91.44923 assigned negative charge : -289.5542 centred at (gu) : 90.53593 89.50288 91.49663 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 51136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17142 grid for indexing accessible points = 1.400000 m= 18333 mr = 35079 m= 2648 mr = 13607 m= 135 mr = 1617 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 641 time to turn everything in is 0.2900000 number of dielectric boundary points 21901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 13769 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) : 0.5957760 object centre at (A) : -12.31450 20.95400 27.10300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4150645E-02 -5.1647294E-02 midg,1,midg; midg,igrid,midg -1.6671209E-02 -2.8379008E-02 1,midg,midg; igrid,midg,midg -1.9140901E-02 -2.4051918E-02 gauss-seidel spectral radius is 0.9983744 estimated iterations to convergence 197 setup time was (sec) 0.6100000 now iterating at: 14:21:45 rms-change max change #iterations 3.200960 160.2591 at 10iterations 1.386515 57.39142 at 20iterations 0.6072749 24.86848 at 30iterations 0.2648173 10.81743 at 40iterations 0.1151804 4.538059 at 50iterations 5.0308589E-02 1.940651 at 60iterations 2.2011999E-02 0.8238831 at 70iterations 9.6329683E-03 0.3932610 at 80iterations 4.2008520E-03 0.1585922 at 90iterations 1.8325420E-03 6.4720154E-02 at 100iterations 8.0126512E-04 3.2546997E-02 at 110iterations 3.4978014E-04 1.3107300E-02 at 120iterations finished qdiffx linear iterations at : 14:21:55 total time elapsed so far: 10.46000 # loops : 120 mean,max change (kT/e) : 3.4978014E-04 1.3107300E-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) 10.59000 DelPhi exited at 14:22:15 10.590u 0.318s 0:30.88 35.2% 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 Wed Dec 21 2011 at 14:22:17 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.680992 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): -34.76100 10.13200 ymin,ymax (A): 0.5979999 41.31000 zmin,zma (A): -2.774000 56.98000 x,y,z range (A): 44.89300 40.71200 59.75400 scale (grids/A): 2.680992 object centre (A): -12.31450 20.95400 27.10300 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 267.6024 centred at (gu) : 91.23164 88.61024 92.17378 assigned negative charge : -289.5542 centred at (gu) : 90.80389 89.25424 92.24497 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 117826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17142 grid for indexing accessible points = 1.400000 m= 59802 mr = 84654 m= 20805 mr = 49032 m= 4563 mr = 16752 m= 650 mr = 3428 m= 32 mr = 421 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2175 time to turn everything in is 0.6700000 number of dielectric boundary points 49383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14063 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) : 1.787328 object centre at (A) : -12.31450 20.95400 27.10300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4916451 -0.8772668 midg,1,midg; midg,igrid,midg -0.2020589 -0.3453178 1,midg,midg; igrid,midg,midg -0.2226345 -0.2859545 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 0.9400000 now iterating at: 14:22:19 rms-change max change #iterations 7.767752 311.0995 at 10iterations 4.374754 121.9412 at 20iterations 2.446983 74.54008 at 30iterations 1.367944 35.54992 at 40iterations 0.7593388 17.69874 at 50iterations 0.4224278 8.878878 at 60iterations 0.2347047 4.812912 at 70iterations 0.1303689 2.769863 at 80iterations 7.2002947E-02 1.609646 at 90iterations 3.9963361E-02 0.8787956 at 100iterations 2.2106703E-02 0.4838276 at 110iterations 1.2257525E-02 0.2813358 at 120iterations 6.8023535E-03 0.1644986 at 130iterations 3.7564014E-03 8.5899353E-02 at 140iterations 2.0802063E-03 5.2062988E-02 at 150iterations 1.1531758E-03 2.6337624E-02 at 160iterations 6.3767523E-04 1.4045954E-02 at 170iterations 3.5297443E-04 7.6904297E-03 at 180iterations finished qdiffx linear iterations at : 14:22:32 total time elapsed so far: 14.40000 # loops : 180 mean,max change (kT/e) : 3.5297443E-04 7.6904297E-03 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 14:22:46 14.539u 0.303s 0:30.22 49.0% 0+0k 0+0io 0pf+0w