Mon Oct 10 00:20:52 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 Mon Oct 10 2011 at 00:20:52 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6247 !!! WARNING: HIR 113 has a net charge of 0.5140 !!! WARNING: HIR 114 has a net charge of 0.5140 !!! WARNING: HIY 151 has a net charge of 0.2000 !!! WARNING: HIY 499 has a net charge of 0.2000 !!! WARNING: ZN6 697 has a net charge of 1.4000 !!! WARNING: ZN6 698 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.4872974 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): -21.13300 51.92300 ymin,ymax (A): 35.52700 93.96000 zmin,zma (A): 40.10100 105.6500 x,y,z range (A): 73.05600 58.43300 65.54900 scale (grids/A): 0.4872974 object centre (A): 15.39500 64.74350 72.87550 number of atom coordinates read : 6247 total number of charged atoms : 5546 net assigned charge : -9.771980 assigned positive charge : 857.5122 centred at (gu) : 90.23007 90.23845 89.92925 assigned negative charge : -867.2921 centred at (gu) : 90.11551 90.31757 90.00682 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8307 nv = 96 ne = 84 npr = 117178 no. pairs analyzed = 117178 no. exposed pairs = 7250 no. arc points = 48985 no. surface atoms = 2434 nbur = 3813 mkacc time = 0.2800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 262 mr = 4240 m= 0 mr = 4 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4480 ## 660 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 11267 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9238189E-11 -1.3128332E-10 midg,1,midg; midg,igrid,midg 3.7419328E-11 -1.4485280E-10 1,midg,midg; igrid,midg,midg -1.6523535E-10 8.3771198E-11 gauss-seidel spectral radius is 0.9785339 estimated iterations to convergence 57 setup time was (sec) 0.8100000 now iterating at: 00:20:53 rms-change max change #iterations 5.8673270E-02 9.615799 at 10iterations 3.2472597E-03 0.4858379 at 20iterations 6.2616332E-04 8.4098816E-02 at 30iterations 2.7184314E-04 3.1677246E-02 at 40iterations 1.2226691E-04 1.3742447E-02 at 50iterations finished qdiffx linear iterations at : 00:20:56 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.2226691E-04 1.3742447E-02 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 00:20:56 3.861u 0.199s 0:04.34 93.3% 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 Mon Oct 10 2011 at 00:20:56 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6247 !!! WARNING: HIR 113 has a net charge of 0.5140 !!! WARNING: HIR 114 has a net charge of 0.5140 !!! WARNING: HIY 151 has a net charge of 0.2000 !!! WARNING: HIY 499 has a net charge of 0.2000 !!! WARNING: ZN6 697 has a net charge of 1.4000 !!! WARNING: ZN6 698 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.461892 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): -21.13300 51.92300 ymin,ymax (A): 35.52700 93.96000 zmin,zma (A): 40.10100 105.6500 x,y,z range (A): 73.05600 58.43300 65.54900 scale (grids/A): 1.461892 object centre (A): 15.39500 64.74350 72.87550 number of atom coordinates read : 6247 total number of charged atoms : 5546 net assigned charge : -9.771980 assigned positive charge : 857.5122 centred at (gu) : 90.68848 90.71385 89.78600 assigned negative charge : -867.2921 centred at (gu) : 90.34634 90.95245 90.02023 start vw surface at 0.2700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 94896 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 25930 mr = 64929 m= 1708 mr = 16614 m= 19 mr = 564 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 497 time to turn everything in is 0.7400000 number of dielectric boundary points 40446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 589 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 40891 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) : 0.4872974 object centre at (A) : 15.39500 64.74350 72.87550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5392617E-03 -7.1882056E-03 midg,1,midg; midg,igrid,midg -9.4405311E-04 -1.7826784E-02 1,midg,midg; igrid,midg,midg -6.5385243E-03 8.7017706E-03 gauss-seidel spectral radius is 0.9979732 estimated iterations to convergence 177 setup time was (sec) 1.040000 now iterating at: 00:20:58 rms-change max change #iterations 3.776741 143.7262 at 10iterations 1.497632 54.38186 at 20iterations 0.5951740 19.36446 at 30iterations 0.2373988 7.499336 at 40iterations 9.4435640E-02 3.071198 at 50iterations 3.7662830E-02 1.474173 at 60iterations 1.5094044E-02 0.4758511 at 70iterations 6.1002686E-03 0.2172241 at 80iterations 2.5810613E-03 8.9607239E-02 at 90iterations 1.2146611E-03 3.8555145E-02 at 100iterations 6.8455341E-04 2.0312309E-02 at 110iterations 4.5359420E-04 1.2840271E-02 at 120iterations finished qdiffx linear iterations at : 00:21:04 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 4.5359420E-04 1.2840271E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 00:21:05 7.747u 0.161s 0:08.38 94.2% 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 Mon Oct 10 2011 at 00:21:05 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6247 !!! WARNING: HIR 113 has a net charge of 0.5140 !!! WARNING: HIR 114 has a net charge of 0.5140 !!! WARNING: HIY 151 has a net charge of 0.2000 !!! WARNING: HIY 499 has a net charge of 0.2000 !!! WARNING: ZN6 697 has a net charge of 1.4000 !!! WARNING: ZN6 698 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.192838 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): -21.13300 51.92300 ymin,ymax (A): 35.52700 93.96000 zmin,zma (A): 40.10100 105.6500 x,y,z range (A): 73.05600 58.43300 65.54900 scale (grids/A): 2.192838 object centre (A): 15.39500 64.74350 72.87550 number of atom coordinates read : 6247 total number of charged atoms : 5546 net assigned charge : -9.771980 assigned positive charge : 857.5122 centred at (gu) : 91.03214 91.07031 89.67855 assigned negative charge : -867.2921 centred at (gu) : 90.51945 91.42867 90.03020 start vw surface at 0.2600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 221492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 95509 mr = 160109 m= 21208 mr = 73329 m= 2147 mr = 14534 m= 71 mr = 1119 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1646 time to turn everything in is 1.690000 number of dielectric boundary points 91322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 44149 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) : 1.461892 object centre at (A) : 15.39500 64.74350 72.87550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3532731E-02 -0.1005081 midg,1,midg; midg,igrid,midg -3.1248078E-02 -0.3561182 1,midg,midg; igrid,midg,midg -1.9742027E-02 6.2821947E-02 gauss-seidel spectral radius is 0.9991425 estimated iterations to convergence 270 setup time was (sec) 1.990000 now iterating at: 00:21:07 rms-change max change #iterations 10.73656 262.3395 at 10iterations 6.185690 144.7236 at 20iterations 3.525933 78.37308 at 30iterations 1.992855 42.76137 at 40iterations 1.123975 24.47421 at 50iterations 0.6312530 13.09987 at 60iterations 0.3526091 7.014330 at 70iterations 0.1968613 3.840899 at 80iterations 0.1094418 2.207747 at 90iterations 6.1004490E-02 1.165471 at 100iterations 3.3755314E-02 0.6485643 at 110iterations 1.8791674E-02 0.3963699 at 120iterations 1.0418432E-02 0.1863642 at 130iterations 5.8208914E-03 0.1069000 at 140iterations 3.2584716E-03 6.6504836E-02 at 150iterations 1.8603434E-03 3.6102295E-02 at 160iterations 1.0963775E-03 2.3525238E-02 at 170iterations 6.8113476E-04 1.2866974E-02 at 180iterations finished qdiffx linear iterations at : 00:21:17 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 6.8113476E-04 1.2866974E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 00:21:18 12.561u 0.190s 0:13.04 97.7% 0+0k 0+0io 0pf+0w