Sun Oct 9 08:00:01 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 Sun Oct 9 2011 at 08:00:01 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7007460 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): 4.360000 49.89900 ymin,ymax (A): -24.74600 26.05700 zmin,zma (A): -19.35800 30.46100 x,y,z range (A): 45.53900 50.80300 49.81900 scale (grids/A): 0.7007460 object centre (A): 27.12950 0.6554995 5.551500 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327990 assigned positive charge : 340.8183 centred at (gu) : 89.99999 91.04829 90.03620 assigned negative charge : -344.1467 centred at (gu) : 90.02488 91.13701 90.13814 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7610 nv = 96 ne = 84 npr = 44425 no. pairs analyzed = 44425 no. exposed pairs = 2930 no. arc points = 20851 no. surface atoms = 972 nbur = 1247 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 536 mr = 4129 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.2600000 number of dielectric boundary points 3925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3745637E-08 -7.2142647E-08 midg,1,midg; midg,igrid,midg 1.4238722E-08 -8.0421934E-08 1,midg,midg; igrid,midg,midg -1.1723061E-08 -3.5051727E-08 gauss-seidel spectral radius is 0.9894117 estimated iterations to convergence 79 setup time was (sec) 0.4800000 now iterating at: 08:00:01 rms-change max change #iterations 0.2083947 30.09791 at 10iterations 2.4807751E-02 3.694698 at 20iterations 2.9793410E-03 0.5030456 at 30iterations 3.5926592E-04 5.1455498E-02 at 40iterations 4.2869615E-05 5.5007935E-03 at 50iterations finished qdiffx linear iterations at : 08:00:04 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.2869615E-05 5.5007935E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 08:00:04 3.098u 0.129s 0:03.50 91.7% 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 Sun Oct 9 2011 at 08:00:04 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.102238 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): 4.360000 49.89900 ymin,ymax (A): -24.74600 26.05700 zmin,zma (A): -19.35800 30.46100 x,y,z range (A): 45.53900 50.80300 49.81900 scale (grids/A): 2.102238 object centre (A): 27.12950 0.6554995 5.551500 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327990 assigned positive charge : 340.8183 centred at (gu) : 89.99947 93.14455 90.10811 assigned negative charge : -344.1467 centred at (gu) : 90.07458 93.41089 90.41422 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20851 grid for indexing accessible points = 1.400000 m= 32078 mr = 54329 m= 6752 mr = 24120 m= 645 mr = 4457 m= 22 mr = 289 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 0.5800000 number of dielectric boundary points 36006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 16511 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) : 0.7007460 object centre at (A) : 27.12950 0.6554995 5.551500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3516187E-04 -4.2173240E-02 midg,1,midg; midg,igrid,midg 2.8180758E-02 -4.0544700E-03 1,midg,midg; igrid,midg,midg -4.0786453E-03 -3.4322970E-02 gauss-seidel spectral radius is 0.9988406 estimated iterations to convergence 232 setup time was (sec) 0.8600000 now iterating at: 08:00:05 rms-change max change #iterations 4.907989 235.3217 at 10iterations 2.429283 100.1822 at 20iterations 1.204324 38.69474 at 30iterations 0.5999632 19.01419 at 40iterations 0.2970680 8.378819 at 50iterations 0.1478132 4.802210 at 60iterations 7.3343225E-02 2.052591 at 70iterations 3.6355980E-02 1.025697 at 80iterations 1.8058345E-02 0.5349789 at 90iterations 8.9758392E-03 0.2703247 at 100iterations 4.4747940E-03 0.1308975 at 110iterations 2.2138373E-03 6.8973541E-02 at 120iterations finished qdiffx linear iterations at : 08:00:12 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 2.2138373E-03 6.8973541E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 08:00:12 7.513u 0.209s 0:07.98 96.6% 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 Sun Oct 9 2011 at 08:00:12 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 3.153357 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): 4.360000 49.89900 ymin,ymax (A): -24.74600 26.05700 zmin,zma (A): -19.35800 30.46100 x,y,z range (A): 45.53900 50.80300 49.81900 scale (grids/A): 3.153357 object centre (A): 27.12950 0.6554995 5.551500 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327990 assigned positive charge : 340.8183 centred at (gu) : 89.99900 94.71674 90.16216 assigned negative charge : -344.1467 centred at (gu) : 90.11192 95.11620 90.62126 start vw surface at 0.1400000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 183460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20851 grid for indexing accessible points = 1.400000 m= 98167 mr = 130922 m= 41772 mr = 80930 m= 12787 mr = 34307 m= 2694 mr = 9884 m= 335 mr = 1812 m= 15 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 3287 time to turn everything in is 1.860000 number of dielectric boundary points 81190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 16616 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) : 2.102238 object centre at (A) : 27.12950 0.6554995 5.551500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6095959E-02 -0.2686102 midg,1,midg; midg,igrid,midg 0.8065572 7.6144613E-02 1,midg,midg; igrid,midg,midg -8.0327563E-02 -0.3013578 gauss-seidel spectral radius is 0.9993038 estimated iterations to convergence 299 setup time was (sec) 2.160000 now iterating at: 08:00:15 rms-change max change #iterations 11.02402 361.6968 at 10iterations 6.509497 138.7668 at 20iterations 3.831480 105.2951 at 30iterations 2.249050 46.75475 at 40iterations 1.321496 25.93690 at 50iterations 0.7754892 15.13884 at 60iterations 0.4542943 7.527411 at 70iterations 0.2659179 4.511094 at 80iterations 0.1555919 2.729354 at 90iterations 9.1126785E-02 1.569057 at 100iterations 5.3226270E-02 0.9147720 at 110iterations 3.1098844E-02 0.5404987 at 120iterations 1.8200142E-02 0.3083496 at 130iterations 1.0632969E-02 0.1732426 at 140iterations 6.2124729E-03 0.1118317 at 150iterations 3.6312516E-03 6.4493179E-02 at 160iterations 2.1248737E-03 3.6640167E-02 at 170iterations 1.2457566E-03 2.1417618E-02 at 180iterations finished qdiffx linear iterations at : 08:00:25 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 1.2457566E-03 2.1417618E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 08:00:26 12.687u 0.220s 0:13.20 97.7% 0+0k 0+0io 0pf+0w