Sat Oct 8 14:13:12 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+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 Sat Oct 8 2011 at 14:13:12 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6307583 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): -11.43400 43.32500 ymin,ymax (A): 10.28600 55.46500 zmin,zma (A): 36.04900 92.48900 x,y,z range (A): 54.75900 45.17900 56.44000 scale (grids/A): 0.6307583 object centre (A): 15.94550 32.87550 64.26900 number of atom coordinates read : 2940 total number of charged atoms : 2794 net assigned charge : -0.9859920 assigned positive charge : 440.3657 centred at (gu) : 89.27192 89.52780 92.09587 assigned negative charge : -441.3525 centred at (gu) : 89.28651 89.42693 92.06349 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7959 nv = 96 ne = 84 npr = 60587 no. pairs analyzed = 60587 no. exposed pairs = 3429 no. arc points = 23656 no. surface atoms = 1173 nbur = 1767 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4720 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2288 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8271470E-09 3.5242251E-09 midg,1,midg; midg,igrid,midg -1.2811603E-08 8.1705469E-09 1,midg,midg; igrid,midg,midg 4.4444748E-10 -2.2350242E-09 gauss-seidel spectral radius is 0.9870077 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 14:13:13 rms-change max change #iterations 0.1512353 23.87189 at 10iterations 1.5034880E-02 2.236538 at 20iterations 1.5839889E-03 0.1896811 at 30iterations 2.3293022E-04 3.3963203E-02 at 40iterations 5.0858209E-05 8.1453323E-03 at 50iterations finished qdiffx linear iterations at : 14:13:17 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 5.0858209E-05 8.1453323E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 14:13:17 4.630u 0.395s 0:05.29 94.8% 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 14:13:17 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.892275 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): -11.43400 43.32500 ymin,ymax (A): 10.28600 55.46500 zmin,zma (A): 36.04900 92.48900 x,y,z range (A): 54.75900 45.17900 56.44000 scale (grids/A): 1.892275 object centre (A): 15.94550 32.87550 64.26900 number of atom coordinates read : 2940 total number of charged atoms : 2794 net assigned charge : -0.9859920 assigned positive charge : 440.3657 centred at (gu) : 87.81524 88.58263 96.28712 assigned negative charge : -441.3525 centred at (gu) : 87.85965 88.28055 96.19048 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23656 grid for indexing accessible points = 1.400000 m= 32594 mr = 63476 m= 4788 mr = 24778 m= 245 mr = 2896 m= 5 mr = 85 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.6800000 number of dielectric boundary points 33600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21985 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) : 0.6307583 object centre at (A) : 15.94550 32.87550 64.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2946493E-02 -2.8036518E-03 midg,1,midg; midg,igrid,midg -5.0811912E-03 1.3842109E-02 1,midg,midg; igrid,midg,midg 8.0712587E-03 7.3980540E-03 gauss-seidel spectral radius is 0.9986476 estimated iterations to convergence 215 setup time was (sec) 0.9800000 now iterating at: 14:13:19 rms-change max change #iterations 4.524796 181.2505 at 10iterations 2.128489 68.11590 at 20iterations 1.003642 35.87766 at 30iterations 0.4709656 14.25118 at 40iterations 0.2217285 6.690826 at 50iterations 0.1043438 3.484596 at 60iterations 4.9219925E-02 1.625814 at 70iterations 2.3227096E-02 0.6647643 at 80iterations 1.0938548E-02 0.3395491 at 90iterations 5.1596025E-03 0.1520348 at 100iterations 2.4454682E-03 7.1296692E-02 at 110iterations 1.1602609E-03 3.3323288E-02 at 120iterations finished qdiffx linear iterations at : 14:13:32 total time elapsed so far: 14.41000 # loops : 120 mean,max change (kT/e) : 1.1602609E-03 3.3323288E-02 energy calculations done at 14.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.61000 DelPhi exited at 14:13:33 14.611u 0.525s 0:15.51 97.5% 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 Sat Oct 8 2011 at 14:13:33 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2940 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.838413 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): -11.43400 43.32500 ymin,ymax (A): 10.28600 55.46500 zmin,zma (A): 36.04900 92.48900 x,y,z range (A): 54.75900 45.17900 56.44000 scale (grids/A): 2.838413 object centre (A): 15.94550 32.87550 64.26900 number of atom coordinates read : 2940 total number of charged atoms : 2794 net assigned charge : -0.9859920 assigned positive charge : 440.3657 centred at (gu) : 86.72289 87.87395 99.43068 assigned negative charge : -441.3525 centred at (gu) : 86.78938 87.42088 99.28569 start vw surface at 0.1300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 201781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23656 grid for indexing accessible points = 1.400000 m= 106548 mr = 153049 m= 38098 mr = 89419 m= 8442 mr = 30838 m= 1027 mr = 6166 m= 43 mr = 623 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.330000 no. cavity mid-points inaccessible to solvent = 629 time to turn everything in is 2.090000 number of dielectric boundary points 75834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 22352 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) : 1.892275 object centre at (A) : 15.94550 32.87550 64.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7611695E-02 4.4077244E-02 midg,1,midg; midg,igrid,midg -2.3323411E-02 0.1688989 1,midg,midg; igrid,midg,midg 0.2136778 0.2676288 gauss-seidel spectral radius is 0.9992674 estimated iterations to convergence 292 setup time was (sec) 2.720000 now iterating at: 14:13:36 rms-change max change #iterations 10.65568 429.6171 at 10iterations 6.256816 115.2025 at 20iterations 3.650633 70.30476 at 30iterations 2.127718 40.88455 at 40iterations 1.236771 20.96189 at 50iterations 0.7181997 13.92590 at 60iterations 0.4163648 7.207989 at 70iterations 0.2407092 4.124916 at 80iterations 0.1392135 2.526156 at 90iterations 8.0432318E-02 1.426339 at 100iterations 4.6496853E-02 0.9142873 at 110iterations 2.6866553E-02 0.4635525 at 120iterations 1.5479939E-02 0.2824335 at 130iterations 8.9532528E-03 0.1466737 at 140iterations 5.1723733E-03 8.8912964E-02 at 150iterations 2.9980997E-03 5.2112579E-02 at 160iterations 1.7389174E-03 2.8247386E-02 at 170iterations 1.0146915E-03 1.7692566E-02 at 180iterations finished qdiffx linear iterations at : 14:14:05 total time elapsed so far: 31.85000 # loops : 180 mean,max change (kT/e) : 1.0146915E-03 1.7692566E-02 energy calculations done at 31.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.03000 DelPhi exited at 14:14:06 32.039u 0.791s 0:33.15 99.0% 0+0k 0+0io 0pf+0w