Wed Dec 21 14:21:12 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+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 Wed Dec 21 2011 at 14:21:12 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6017274 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): -8.713000 50.45000 ymin,ymax (A): 8.852000 49.31200 zmin,zma (A): -4.266000 38.83600 x,y,z range (A): 59.16300 40.46000 43.10200 scale (grids/A): 0.6017274 object centre (A): 20.86850 29.08200 17.28500 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681011 assigned positive charge : 286.9441 centred at (gu) : 89.89723 89.39863 90.51285 assigned negative charge : -282.2633 centred at (gu) : 89.88074 89.28277 90.67353 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4751 nv = 96 ne = 84 npr = 40451 no. pairs analyzed = 40451 no. exposed pairs = 2525 no. arc points = 17605 no. surface atoms = 854 nbur = 1105 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 220 mr = 2555 m= 0 mr = 13 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1851 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 5868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8680998E-09 -2.7237821E-09 midg,1,midg; midg,igrid,midg -1.2942472E-09 4.6939035E-09 1,midg,midg; igrid,midg,midg 1.7513543E-09 2.5767510E-09 gauss-seidel spectral radius is 0.9856514 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 14:21:13 rms-change max change #iterations 9.4327629E-02 17.51401 at 10iterations 7.7649457E-03 1.497559 at 20iterations 6.7133037E-04 0.1163645 at 30iterations 5.6003228E-05 9.4833374E-03 at 40iterations 4.7683939E-06 9.8669529E-04 at 50iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 4.7683939E-06 9.8669529E-04 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 14:21:19 4.004u 0.249s 0:08.14 52.0% 0+0k 0+0io 6pf+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 14:21:21 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.805182 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): -8.713000 50.45000 ymin,ymax (A): 8.852000 49.31200 zmin,zma (A): -4.266000 38.83600 x,y,z range (A): 59.16300 40.46000 43.10200 scale (grids/A): 1.805182 object centre (A): 20.86850 29.08200 17.28500 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681011 assigned positive charge : 286.9441 centred at (gu) : 89.69182 88.19601 91.53864 assigned negative charge : -282.2633 centred at (gu) : 89.64229 87.84852 92.02066 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 51748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17605 grid for indexing accessible points = 1.400000 m= 16978 mr = 35058 m= 1953 mr = 12436 m= 90 mr = 1044 m= 0 mr = 19 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 22212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14283 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) : 0.6017274 object centre at (A) : 20.86850 29.08200 17.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0775821E-02 -5.3082486E-03 midg,1,midg; midg,igrid,midg 1.7568192E-03 6.1384425E-03 1,midg,midg; igrid,midg,midg 3.6586974E-02 3.6226820E-02 gauss-seidel spectral radius is 0.9984062 estimated iterations to convergence 199 setup time was (sec) 0.8000000 now iterating at: 14:21:22 rms-change max change #iterations 3.165840 159.8747 at 10iterations 1.393072 55.82006 at 20iterations 0.6120497 24.81041 at 30iterations 0.2698945 9.977310 at 40iterations 0.1189376 5.021032 at 50iterations 5.2391503E-02 2.024296 at 60iterations 2.3033477E-02 1.035244 at 70iterations 1.0148236E-02 0.3983226 at 80iterations 4.4675614E-03 0.1784706 at 90iterations 1.9664704E-03 7.4747086E-02 at 100iterations 8.6470350E-04 3.4549713E-02 at 110iterations 3.8197075E-04 1.3900757E-02 at 120iterations finished qdiffx linear iterations at : 14:21:32 total time elapsed so far: 9.960000 # loops : 120 mean,max change (kT/e) : 3.8197075E-04 1.3900757E-02 energy calculations done at 9.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 14:21:35 10.124u 0.351s 0:14.50 72.2% 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 14:21:36 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.707773 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): -8.713000 50.45000 ymin,ymax (A): 8.852000 49.31200 zmin,zma (A): -4.266000 38.83600 x,y,z range (A): 59.16300 40.46000 43.10200 scale (grids/A): 2.707773 object centre (A): 20.86850 29.08200 17.28500 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681011 assigned positive charge : 286.9441 centred at (gu) : 89.53767 87.29410 92.30791 assigned negative charge : -282.2633 centred at (gu) : 89.46349 86.77271 93.03108 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 119874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17605 grid for indexing accessible points = 1.400000 m= 57118 mr = 85151 m= 17825 mr = 46387 m= 3154 mr = 14271 m= 358 mr = 2213 m= 17 mr = 209 m= 0 mr = 4 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 50111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 14606 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) : 1.805182 object centre at (A) : 20.86850 29.08200 17.28500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1003355 -4.3058805E-02 midg,1,midg; midg,igrid,midg 5.1522840E-02 4.7642216E-02 1,midg,midg; igrid,midg,midg 0.4582684 0.3612036 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.600000 now iterating at: 14:21:39 rms-change max change #iterations 7.738138 276.1188 at 10iterations 4.416200 152.9164 at 20iterations 2.492114 58.16779 at 30iterations 1.394763 32.12944 at 40iterations 0.7805274 17.32886 at 50iterations 0.4368172 10.06970 at 60iterations 0.2436545 5.332843 at 70iterations 0.1356007 2.936827 at 80iterations 7.5585872E-02 1.626879 at 90iterations 4.2241409E-02 1.033901 at 100iterations 2.3457801E-02 0.5392876 at 110iterations 1.3086009E-02 0.2832336 at 120iterations 7.2747134E-03 0.1507494 at 130iterations 4.0376708E-03 9.2018068E-02 at 140iterations 2.2512367E-03 4.7527313E-02 at 150iterations 1.2505930E-03 3.0038834E-02 at 160iterations 6.9344026E-04 1.5785217E-02 at 170iterations 3.8614852E-04 8.0623627E-03 at 180iterations finished qdiffx linear iterations at : 14:21:53 total time elapsed so far: 16.26000 # loops : 180 mean,max change (kT/e) : 3.8614852E-04 8.0623627E-03 energy calculations done at 16.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.45000 DelPhi exited at 14:22:00 16.453u 0.540s 0:23.80 71.3% 0+0k 0+0io 0pf+0w