Sat Oct 8 18:44:55 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 18:44:55 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 497 has a net charge of 1.4000 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: 0.6207822 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): -31.99500 17.65700 ymin,ymax (A): -23.75400 23.06100 zmin,zma (A): -12.52500 44.82200 x,y,z range (A): 49.65200 46.81500 57.34700 scale (grids/A): 0.6207822 object centre (A): -7.169001 -0.3465004 16.14850 number of atom coordinates read : 2589 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 88.54803 89.26889 89.80466 assigned negative charge : -388.3386 centred at (gu) : 88.45293 89.29787 89.68681 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6619 nv = 96 ne = 84 npr = 53802 no. pairs analyzed = 53802 no. exposed pairs = 2977 no. arc points = 21589 no. surface atoms = 1000 nbur = 1589 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3747 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.3500000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9963016E-09 1.0744544E-08 midg,1,midg; midg,igrid,midg 6.2006853E-09 1.1746548E-09 1,midg,midg; igrid,midg,midg -4.5155071E-09 7.0717845E-09 gauss-seidel spectral radius is 0.9865574 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 18:44:56 rms-change max change #iterations 0.1307827 20.83912 at 10iterations 1.2038098E-02 1.691803 at 20iterations 1.1144116E-03 0.1795959 at 30iterations 1.0333431E-04 1.5510559E-02 at 40iterations 9.7630027E-06 1.3961792E-03 at 50iterations finished qdiffx linear iterations at : 18:44:59 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 9.7630027E-06 1.3961792E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 18:45:00 4.332u 0.230s 0:04.83 94.4% 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 18:45:00 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 497 has a net charge of 1.4000 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: 1.862347 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): -31.99500 17.65700 ymin,ymax (A): -23.75400 23.06100 zmin,zma (A): -12.52500 44.82200 x,y,z range (A): 49.65200 46.81500 57.34700 scale (grids/A): 1.862347 object centre (A): -7.169001 -0.3465004 16.14850 number of atom coordinates read : 2589 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 85.64351 87.80641 89.41378 assigned negative charge : -388.3386 centred at (gu) : 85.35857 87.89340 89.06014 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21589 grid for indexing accessible points = 1.400000 m= 25971 mr = 50496 m= 3679 mr = 19457 m= 206 mr = 2289 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 3418 time to turn everything in is 0.6400000 number of dielectric boundary points 29145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19222 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) : 0.6207822 object centre at (A) : -7.169001 -0.3465004 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7228540E-02 2.5711412E-02 midg,1,midg; midg,igrid,midg 1.2515255E-02 2.3084616E-03 1,midg,midg; igrid,midg,midg -3.6323534E-03 2.9076625E-02 gauss-seidel spectral radius is 0.9985698 estimated iterations to convergence 210 setup time was (sec) 0.9600000 now iterating at: 18:45:01 rms-change max change #iterations 4.064686 189.4152 at 10iterations 1.868371 65.90126 at 20iterations 0.8589182 27.81430 at 30iterations 0.3942294 13.13759 at 40iterations 0.1824931 6.228180 at 50iterations 8.3858550E-02 2.877228 at 60iterations 3.8555376E-02 1.198730 at 70iterations 1.7819248E-02 0.5885944 at 80iterations 8.1501957E-03 0.2682422 at 90iterations 3.7688853E-03 0.1294708 at 100iterations 1.7351145E-03 5.3459167E-02 at 110iterations 7.9961162E-04 2.8438568E-02 at 120iterations finished qdiffx linear iterations at : 18:45:10 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 7.9961162E-04 2.8438568E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 18:45:10 9.661u 0.266s 0:10.23 96.9% 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 18:45:10 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 497 has a net charge of 1.4000 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: 2.793520 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): -31.99500 17.65700 ymin,ymax (A): -23.75400 23.06100 zmin,zma (A): -12.52500 44.82200 x,y,z range (A): 49.65200 46.81500 57.34700 scale (grids/A): 2.793520 object centre (A): -7.169001 -0.3465004 16.14850 number of atom coordinates read : 2589 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 392.2440 centred at (gu) : 83.46510 86.70950 89.12071 assigned negative charge : -388.3386 centred at (gu) : 83.03790 86.84011 88.59019 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 165583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21589 grid for indexing accessible points = 1.400000 m= 84726 mr = 121739 m= 29695 mr = 70369 m= 6528 mr = 24076 m= 824 mr = 4922 m= 60 mr = 541 m= 1 mr = 22 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 11672 time to turn everything in is 1.370000 number of dielectric boundary points 65749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 19599 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) : 1.862347 object centre at (A) : -7.169001 -0.3465004 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9623196E-02 0.3171508 midg,1,midg; midg,igrid,midg 0.1562841 8.6036453E-04 1,midg,midg; igrid,midg,midg -2.8813362E-02 0.3916779 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.710000 now iterating at: 18:45:12 rms-change max change #iterations 9.500691 412.7943 at 10iterations 5.451669 153.0060 at 20iterations 3.113272 71.45903 at 30iterations 1.772804 37.84272 at 40iterations 1.010699 18.81946 at 50iterations 0.5748207 10.99489 at 60iterations 0.3276625 5.918850 at 70iterations 0.1861566 3.540794 at 80iterations 0.1058805 1.979528 at 90iterations 6.0155693E-02 1.086897 at 100iterations 3.4270093E-02 0.6775665 at 110iterations 1.9447908E-02 0.3448120 at 120iterations 1.1056733E-02 0.2139740 at 130iterations 6.3015763E-03 0.1238251 at 140iterations 3.5841323E-03 7.5784683E-02 at 150iterations 2.0344837E-03 3.8734436E-02 at 160iterations 1.1603791E-03 2.1583557E-02 at 170iterations 6.5901107E-04 1.1962891E-02 at 180iterations finished qdiffx linear iterations at : 18:45:26 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 6.5901107E-04 1.1962891E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 18:45:26 15.426u 0.274s 0:16.01 98.0% 0+0k 0+0io 0pf+0w