Sat Oct 8 20:55:35 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 20:55:35 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! 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 435 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6461332 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): -32.10100 17.58700 ymin,ymax (A): -23.19900 23.44200 zmin,zma (A): -12.63300 42.46400 x,y,z range (A): 49.68800 46.64100 55.09700 scale (grids/A): 0.6461332 object centre (A): -7.256999 0.1215000 14.91550 number of atom coordinates read : 2524 total number of charged atoms : 2380 net assigned charge : 2.406008 assigned positive charge : 379.0513 centred at (gu) : 88.66162 89.11075 90.24229 assigned negative charge : -376.6456 centred at (gu) : 88.53845 89.13921 90.16483 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6994 nv = 96 ne = 84 npr = 52640 no. pairs analyzed = 52640 no. exposed pairs = 2952 no. arc points = 21094 no. surface atoms = 987 nbur = 1537 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3971 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.1900000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2038 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7274296E-09 1.5362129E-08 midg,1,midg; midg,igrid,midg 9.8210631E-09 4.9282323E-10 1,midg,midg; igrid,midg,midg -1.6529137E-08 1.5467549E-08 gauss-seidel spectral radius is 0.9875793 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 20:55:36 rms-change max change #iterations 0.1505442 30.41879 at 10iterations 1.5371394E-02 2.173556 at 20iterations 1.5714711E-03 0.2287788 at 30iterations 1.6675866E-04 2.2361755E-02 at 40iterations 1.8315357E-05 2.6779175E-03 at 50iterations finished qdiffx linear iterations at : 20:55:39 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.8315357E-05 2.6779175E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 20:55:39 3.693u 0.217s 0:04.18 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 Sat Oct 8 2011 at 20:55:39 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! 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 435 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.938400 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): -32.10100 17.58700 ymin,ymax (A): -23.19900 23.44200 zmin,zma (A): -12.63300 42.46400 x,y,z range (A): 49.68800 46.64100 55.09700 scale (grids/A): 1.938400 object centre (A): -7.256999 0.1215000 14.91550 number of atom coordinates read : 2524 total number of charged atoms : 2380 net assigned charge : 2.406008 assigned positive charge : 379.0513 centred at (gu) : 85.98434 87.33167 90.72655 assigned negative charge : -376.6456 centred at (gu) : 85.61520 87.41749 90.49445 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21094 grid for indexing accessible points = 1.400000 m= 27636 mr = 53179 m= 4323 mr = 20666 m= 220 mr = 2731 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 3349 time to turn everything in is 0.3800000 number of dielectric boundary points 30942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18759 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) : 0.6461332 object centre at (A) : -7.256999 0.1215000 14.91550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2569248E-02 -3.4587455E-03 midg,1,midg; midg,igrid,midg 1.4149887E-02 -2.4185944E-03 1,midg,midg; igrid,midg,midg -4.9342820E-03 4.3415748E-02 gauss-seidel spectral radius is 0.9986728 estimated iterations to convergence 217 setup time was (sec) 0.6000000 now iterating at: 20:55:40 rms-change max change #iterations 4.284407 189.8238 at 10iterations 2.029502 68.28276 at 20iterations 0.9613766 32.99353 at 30iterations 0.4566054 14.12976 at 40iterations 0.2165079 6.770657 at 50iterations 0.1026986 3.124088 at 60iterations 4.8553351E-02 1.522652 at 70iterations 2.2976462E-02 0.7518272 at 80iterations 1.0883096E-02 0.3456898 at 90iterations 5.1489458E-03 0.1739140 at 100iterations 2.4443418E-03 8.3992004E-02 at 110iterations 1.1579475E-03 4.2831421E-02 at 120iterations finished qdiffx linear iterations at : 20:55:48 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 1.1579475E-03 4.2831421E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 20:55:48 8.434u 0.249s 0:08.96 96.7% 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 Sat Oct 8 2011 at 20:55:48 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! 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 435 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.907599 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): -32.10100 17.58700 ymin,ymax (A): -23.19900 23.44200 zmin,zma (A): -12.63300 42.46400 x,y,z range (A): 49.68800 46.64100 55.09700 scale (grids/A): 2.907599 object centre (A): -7.256999 0.1215000 14.91550 number of atom coordinates read : 2524 total number of charged atoms : 2380 net assigned charge : 2.406008 assigned positive charge : 379.0513 centred at (gu) : 83.97636 85.99727 91.08966 assigned negative charge : -376.6456 centred at (gu) : 83.42271 86.12620 90.74178 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 174362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21094 grid for indexing accessible points = 1.400000 m= 89113 mr = 128312 m= 32457 mr = 73824 m= 7884 mr = 26402 m= 986 mr = 5919 m= 49 mr = 612 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 11116 time to turn everything in is 0.9900000 number of dielectric boundary points 69763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19039 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) : 1.938400 object centre at (A) : -7.256999 0.1215000 14.91550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1169566 -2.6762765E-02 midg,1,midg; midg,igrid,midg 0.1380776 -6.7084886E-02 1,midg,midg; igrid,midg,midg 2.0705799E-02 0.5116384 gauss-seidel spectral radius is 0.9992610 estimated iterations to convergence 290 setup time was (sec) 1.260000 now iterating at: 20:55:50 rms-change max change #iterations 9.937017 481.5416 at 10iterations 5.779026 163.2170 at 20iterations 3.344728 80.36009 at 30iterations 1.935870 38.96114 at 40iterations 1.118943 21.80546 at 50iterations 0.6472812 12.48769 at 60iterations 0.3725772 7.507167 at 70iterations 0.2145908 4.016859 at 80iterations 0.1235209 2.402386 at 90iterations 7.1243279E-02 1.299578 at 100iterations 4.1075006E-02 0.8486748 at 110iterations 2.3654334E-02 0.4490051 at 120iterations 1.3620570E-02 0.2333107 at 130iterations 7.8610769E-03 0.1432610 at 140iterations 4.5448099E-03 8.2508087E-02 at 150iterations 2.6375686E-03 4.8385620E-02 at 160iterations 1.5413137E-03 3.1286240E-02 at 170iterations 9.0579683E-04 1.7715454E-02 at 180iterations finished qdiffx linear iterations at : 20:56:02 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 9.0579683E-04 1.7715454E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 20:56:03 13.771u 0.270s 0:14.32 98.0% 0+0k 0+0io 0pf+0w