Tue Oct 11 04:52:44 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+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 Tue Oct 11 2011 at 04:52:44 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 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: 0.6850106 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): -2.964000 49.00600 ymin,ymax (A): -10.16700 36.18200 zmin,zma (A): -18.61900 18.17500 x,y,z range (A): 51.97000 46.34900 36.79400 scale (grids/A): 0.6850106 object centre (A): 23.02100 13.00750 -0.2219992 number of atom coordinates read : 2112 total number of charged atoms : 1972 net assigned charge : 6.500009 assigned positive charge : 319.9309 centred at (gu) : 91.06139 91.32999 90.00208 assigned negative charge : -313.4312 centred at (gu) : 91.04556 91.17844 90.03025 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6392 nv = 96 ne = 84 npr = 43816 no. pairs analyzed = 43816 no. exposed pairs = 2399 no. arc points = 16428 no. surface atoms = 825 nbur = 1287 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3703 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1533 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7462 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9248341E-08 2.2617536E-08 midg,1,midg; midg,igrid,midg -1.0707604E-08 9.8225584E-08 1,midg,midg; igrid,midg,midg 2.1471861E-08 4.3886597E-08 gauss-seidel spectral radius is 0.9888939 estimated iterations to convergence 77 setup time was (sec) 0.4700000 now iterating at: 04:52:45 rms-change max change #iterations 0.1730153 24.08368 at 10iterations 2.0403236E-02 3.059814 at 20iterations 2.3960725E-03 0.3354769 at 30iterations 2.9559605E-04 4.0256500E-02 at 40iterations 4.2997064E-05 6.0672760E-03 at 50iterations finished qdiffx linear iterations at : 04:52:48 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 4.2997064E-05 6.0672760E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 04:52:48 3.310u 0.223s 0:04.03 87.5% 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 Tue Oct 11 2011 at 04:52:48 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 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: 2.055032 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): -2.964000 49.00600 ymin,ymax (A): -10.16700 36.18200 zmin,zma (A): -18.61900 18.17500 x,y,z range (A): 51.97000 46.34900 36.79400 scale (grids/A): 2.055032 object centre (A): 23.02100 13.00750 -0.2219992 number of atom coordinates read : 2112 total number of charged atoms : 1972 net assigned charge : 6.500009 assigned positive charge : 319.9309 centred at (gu) : 93.18395 93.99004 90.00627 assigned negative charge : -313.4312 centred at (gu) : 93.13670 93.53516 90.09081 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16428 grid for indexing accessible points = 1.400000 m= 25728 mr = 49737 m= 4357 mr = 19290 m= 318 mr = 2732 m= 11 mr = 134 m= 0 mr = 1 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 27650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15620 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) : 0.6850106 object centre at (A) : 23.02100 13.00750 -0.2219992 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6714647E-02 1.1712924E-02 midg,1,midg; midg,igrid,midg -4.5426529E-02 5.0468180E-02 1,midg,midg; igrid,midg,midg 3.6476817E-02 9.0162925E-02 gauss-seidel spectral radius is 0.9987550 estimated iterations to convergence 224 setup time was (sec) 0.8100000 now iterating at: 04:52:49 rms-change max change #iterations 4.333853 187.8406 at 10iterations 2.102141 72.43419 at 20iterations 1.018636 33.10125 at 30iterations 0.4958402 15.11554 at 40iterations 0.2408826 7.763901 at 50iterations 0.1170164 3.534907 at 60iterations 5.6796104E-02 1.832165 at 70iterations 2.7559141E-02 0.8445969 at 80iterations 1.3455844E-02 0.4028625 at 90iterations 6.5164375E-03 0.2037888 at 100iterations 3.1863146E-03 0.1005478 at 110iterations 1.5651127E-03 5.3779602E-02 at 120iterations finished qdiffx linear iterations at : 04:52:56 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.5651127E-03 5.3779602E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 04:52:57 7.940u 0.286s 0:08.68 94.7% 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 Tue Oct 11 2011 at 04:52:57 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 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: 3.082548 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): -2.964000 49.00600 ymin,ymax (A): -10.16700 36.18200 zmin,zma (A): -18.61900 18.17500 x,y,z range (A): 51.97000 46.34900 36.79400 scale (grids/A): 3.082548 object centre (A): 23.02100 13.00750 -0.2219992 number of atom coordinates read : 2112 total number of charged atoms : 1972 net assigned charge : 6.500009 assigned positive charge : 319.9309 centred at (gu) : 94.77586 95.98492 90.00943 assigned negative charge : -313.4312 centred at (gu) : 94.70501 95.30284 90.13627 start vw surface at 0.1200000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 159805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16428 grid for indexing accessible points = 1.400000 m= 82882 mr = 119909 m= 30840 mr = 68842 m= 7755 mr = 24876 m= 1286 mr = 5853 m= 151 mr = 873 m= 4 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 62279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 15776 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) : 2.055032 object centre at (A) : 23.02100 13.00750 -0.2219992 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1480922 9.4298355E-02 midg,1,midg; midg,igrid,midg -0.6165290 0.4583150 1,midg,midg; igrid,midg,midg 0.2162991 1.527431 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 1.870000 now iterating at: 04:52:59 rms-change max change #iterations 9.785694 448.2358 at 10iterations 5.715855 117.6582 at 20iterations 3.333951 73.17072 at 30iterations 1.944168 35.29383 at 40iterations 1.126867 21.17290 at 50iterations 0.6556916 12.16303 at 60iterations 0.3807701 7.428917 at 70iterations 0.2207012 3.965891 at 80iterations 0.1281911 2.263517 at 90iterations 7.4194349E-02 1.307727 at 100iterations 4.3052755E-02 0.7861919 at 110iterations 2.5009610E-02 0.4886436 at 120iterations 1.4593150E-02 0.2762852 at 130iterations 8.5769808E-03 0.1475067 at 140iterations 5.0946786E-03 9.6881866E-02 at 150iterations 3.0792244E-03 6.0363770E-02 at 160iterations 1.9220179E-03 3.8867950E-02 at 170iterations 1.2530278E-03 2.7921677E-02 at 180iterations finished qdiffx linear iterations at : 04:53:10 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 1.2530278E-03 2.7921677E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 04:53:10 12.500u 0.297s 0:13.30 96.1% 0+0k 0+0io 0pf+0w