Tue Oct 11 06:33:13 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 Tue Oct 11 2011 at 06:33:13 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7222853 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): -3.0000210E-03 40.88500 ymin,ymax (A): -18.29000 26.17700 zmin,zma (A): -14.94800 34.34000 x,y,z range (A): 40.88800 44.46700 49.28800 scale (grids/A): 0.7222853 object centre (A): 20.44100 3.943501 9.696000 number of atom coordinates read : 2064 total number of charged atoms : 1926 net assigned charge : 5.851009 assigned positive charge : 315.1781 centred at (gu) : 89.10684 90.20119 89.20179 assigned negative charge : -309.3271 centred at (gu) : 89.04932 90.06540 89.13705 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7341 nv = 96 ne = 84 npr = 41761 no. pairs analyzed = 41761 no. exposed pairs = 2441 no. arc points = 16810 no. surface atoms = 832 nbur = 1232 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4275 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9763841E-08 9.7937260E-08 midg,1,midg; midg,igrid,midg -2.1933404E-08 1.6728876E-07 1,midg,midg; igrid,midg,midg 3.6130821E-08 9.2160988E-08 gauss-seidel spectral radius is 0.9900010 estimated iterations to convergence 81 setup time was (sec) 0.5100000 now iterating at: 06:33:13 rms-change max change #iterations 0.2227018 29.10903 at 10iterations 2.9559478E-02 4.400110 at 20iterations 4.0626414E-03 0.5697708 at 30iterations 6.7704264E-04 9.0736389E-02 at 40iterations 1.5593403E-04 1.7753601E-02 at 50iterations finished qdiffx linear iterations at : 06:33:16 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.5593403E-04 1.7753601E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 06:33:17 3.447u 0.213s 0:03.96 92.1% 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 06:33:17 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.166856 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): -3.0000210E-03 40.88500 ymin,ymax (A): -18.29000 26.17700 zmin,zma (A): -14.94800 34.34000 x,y,z range (A): 40.88800 44.46700 49.28800 scale (grids/A): 2.166856 object centre (A): 20.44100 3.943501 9.696000 number of atom coordinates read : 2064 total number of charged atoms : 1926 net assigned charge : 5.851009 assigned positive charge : 315.1781 centred at (gu) : 87.32065 90.60371 87.60522 assigned negative charge : -309.3271 centred at (gu) : 87.14809 90.19655 87.41116 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16810 grid for indexing accessible points = 1.400000 m= 31424 mr = 55676 m= 6335 mr = 24079 m= 631 mr = 4363 m= 13 mr = 344 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 31517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15314 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) : 0.7222853 object centre at (A) : 20.44100 3.943501 9.696000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6212610E-02 3.9198592E-02 midg,1,midg; midg,igrid,midg 8.2270764E-03 5.4601330E-02 1,midg,midg; igrid,midg,midg 2.8758574E-02 2.2269759E-02 gauss-seidel spectral radius is 0.9988684 estimated iterations to convergence 235 setup time was (sec) 0.9600000 now iterating at: 06:33:18 rms-change max change #iterations 4.795338 207.5355 at 10iterations 2.404119 84.40356 at 20iterations 1.213056 41.85320 at 30iterations 0.6116508 18.85743 at 40iterations 0.3065045 8.903724 at 50iterations 0.1542577 5.485369 at 60iterations 7.7655524E-02 2.215816 at 70iterations 3.9099172E-02 1.147353 at 80iterations 1.9765152E-02 0.5399246 at 90iterations 1.0061415E-02 0.2967463 at 100iterations 5.0946684E-03 0.1493835 at 110iterations 2.6439973E-03 8.0429077E-02 at 120iterations finished qdiffx linear iterations at : 06:33:25 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 2.6439973E-03 8.0429077E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 06:33:26 8.257u 0.204s 0:08.89 95.0% 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 06:33:26 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.250284 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): -3.0000210E-03 40.88500 ymin,ymax (A): -18.29000 26.17700 zmin,zma (A): -14.94800 34.34000 x,y,z range (A): 40.88800 44.46700 49.28800 scale (grids/A): 3.250284 object centre (A): 20.44100 3.943501 9.696000 number of atom coordinates read : 2064 total number of charged atoms : 1926 net assigned charge : 5.851009 assigned positive charge : 315.1781 centred at (gu) : 85.98093 90.90562 86.40787 assigned negative charge : -309.3271 centred at (gu) : 85.72205 90.29484 86.11680 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 178529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16810 grid for indexing accessible points = 1.400000 m= 97692 mr = 133586 m= 40320 mr = 81749 m= 12233 mr = 33558 m= 2758 mr = 9654 m= 361 mr = 2103 m= 15 mr = 261 m= 0 mr = 3 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 70994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 15408 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) : 2.166856 object centre at (A) : 20.44100 3.943501 9.696000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2203914 0.1153785 midg,1,midg; midg,igrid,midg 5.8500692E-02 0.4355558 1,midg,midg; igrid,midg,midg 0.2724341 0.1611001 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 2.270000 now iterating at: 06:33:28 rms-change max change #iterations 10.52851 364.9583 at 10iterations 6.261138 143.8477 at 20iterations 3.715399 75.19776 at 30iterations 2.203718 50.67445 at 40iterations 1.300830 23.88126 at 50iterations 0.7670744 15.03638 at 60iterations 0.4522772 8.154484 at 70iterations 0.2664640 5.058971 at 80iterations 0.1569330 2.748062 at 90iterations 9.2684954E-02 1.653355 at 100iterations 5.4575302E-02 1.047947 at 110iterations 3.2358736E-02 0.5786417 at 120iterations 1.9357376E-02 0.3278160 at 130iterations 1.1736632E-02 0.2211876 at 140iterations 7.3268791E-03 0.1243362 at 150iterations 4.7737951E-03 9.3528748E-02 at 160iterations 3.2608164E-03 6.8786621E-02 at 170iterations 2.3618594E-03 4.1755676E-02 at 180iterations finished qdiffx linear iterations at : 06:33:39 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 2.3618594E-03 4.1755676E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 06:33:40 13.150u 0.272s 0:13.94 96.2% 0+0k 0+0io 0pf+0w