Tue Oct 11 06:48:15 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 06:48:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 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: 0.5466327 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): -19.83100 45.29500 ymin,ymax (A): 21.51400 78.67300 zmin,zma (A): -72.22100 -24.67700 x,y,z range (A): 65.12600 57.15900 47.54400 scale (grids/A): 0.5466327 object centre (A): 12.73200 50.09350 -48.44900 number of atom coordinates read : 2972 total number of charged atoms : 2832 net assigned charge : -2.499990 assigned positive charge : 433.5355 centred at (gu) : 89.33178 89.72884 90.48328 assigned negative charge : -436.0362 centred at (gu) : 89.30318 89.86273 90.48293 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5766 nv = 96 ne = 84 npr = 61030 no. pairs analyzed = 61030 no. exposed pairs = 3709 no. arc points = 25940 no. surface atoms = 1255 nbur = 1717 mkacc time = 0.1000000 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 = 1.568000 m= 229 mr = 3050 m= 0 mr = 13 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2637 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7584 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4493255E-10 -1.7736174E-10 midg,1,midg; midg,igrid,midg 7.7041140E-10 -9.9978192E-10 1,midg,midg; igrid,midg,midg -4.1522435E-10 2.4322233E-11 gauss-seidel spectral radius is 0.9827470 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 06:48:16 rms-change max change #iterations 7.2337814E-02 13.90602 at 10iterations 4.8278295E-03 0.8817883 at 20iterations 3.3711936E-04 5.0813675E-02 at 30iterations 2.5332871E-05 5.2185059E-03 at 40iterations 2.6895975E-06 5.5408478E-04 at 50iterations finished qdiffx linear iterations at : 06:48:19 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.6895975E-06 5.5408478E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 06:48:19 3.437u 0.178s 0:04.01 89.7% 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 06:48:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.639898 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): -19.83100 45.29500 ymin,ymax (A): 21.51400 78.67300 zmin,zma (A): -72.22100 -24.67700 x,y,z range (A): 65.12600 57.15900 47.54400 scale (grids/A): 1.639898 object centre (A): 12.73200 50.09350 -48.44900 number of atom coordinates read : 2972 total number of charged atoms : 2832 net assigned charge : -2.499990 assigned positive charge : 433.5355 centred at (gu) : 87.99483 89.18579 91.44954 assigned negative charge : -436.0362 centred at (gu) : 87.90926 89.58788 91.44824 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20208 mr = 43416 m= 2086 mr = 14322 m= 44 mr = 1129 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 321 time to turn everything in is 0.3200000 number of dielectric boundary points 27356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21746 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) : 0.5466327 object centre at (A) : 12.73200 50.09350 -48.44900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5252866E-03 8.1632826E-03 midg,1,midg; midg,igrid,midg -4.8987172E-03 3.2241654E-03 1,midg,midg; igrid,midg,midg -5.8222166E-03 -2.9920220E-02 gauss-seidel spectral radius is 0.9982044 estimated iterations to convergence 187 setup time was (sec) 0.5400000 now iterating at: 06:48:20 rms-change max change #iterations 3.302292 189.1646 at 10iterations 1.380746 51.16815 at 20iterations 0.5787964 23.03714 at 30iterations 0.2431214 8.822704 at 40iterations 0.1018035 3.712219 at 50iterations 4.2678293E-02 1.538931 at 60iterations 1.7885957E-02 0.6535721 at 70iterations 7.4957004E-03 0.2678007 at 80iterations 3.1521409E-03 0.1058302 at 90iterations 1.3183644E-03 4.9056053E-02 at 100iterations 5.5576552E-04 2.2949219E-02 at 110iterations 2.3314058E-04 8.8729858E-03 at 120iterations finished qdiffx linear iterations at : 06:48:27 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.3314058E-04 8.8729858E-03 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 06:48:28 7.816u 0.195s 0:08.44 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 06:48:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.459847 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): -19.83100 45.29500 ymin,ymax (A): 21.51400 78.67300 zmin,zma (A): -72.22100 -24.67700 x,y,z range (A): 65.12600 57.15900 47.54400 scale (grids/A): 2.459847 object centre (A): 12.73200 50.09350 -48.44900 number of atom coordinates read : 2972 total number of charged atoms : 2832 net assigned charge : -2.499990 assigned positive charge : 433.5355 centred at (gu) : 86.99215 88.77856 92.17417 assigned negative charge : -436.0362 centred at (gu) : 86.86374 89.38174 92.17227 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 148329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69356 mr = 106040 m= 20283 mr = 55665 m= 3252 mr = 15678 m= 233 mr = 2325 m= 7 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1022 time to turn everything in is 0.7900000 number of dielectric boundary points 61628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22636 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) : 1.639898 object centre at (A) : 12.73200 50.09350 -48.44900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4093370E-02 0.1508609 midg,1,midg; midg,igrid,midg -6.8385616E-02 6.0805682E-02 1,midg,midg; igrid,midg,midg -9.4684549E-02 -0.8176730 gauss-seidel spectral radius is 0.9991463 estimated iterations to convergence 270 setup time was (sec) 1.030000 now iterating at: 06:48:29 rms-change max change #iterations 8.513034 262.9201 at 10iterations 4.772962 150.0821 at 20iterations 2.666094 66.94174 at 30iterations 1.483581 38.22943 at 40iterations 0.8262466 17.77188 at 50iterations 0.4568361 10.57115 at 60iterations 0.2524729 6.700809 at 70iterations 0.1395767 3.022103 at 80iterations 7.7138953E-02 1.690290 at 90iterations 4.2427767E-02 0.9312744 at 100iterations 2.3402110E-02 0.4808278 at 110iterations 1.2904617E-02 0.2653255 at 120iterations 7.0983157E-03 0.1486282 at 130iterations 3.9212555E-03 7.7293396E-02 at 140iterations 2.1572241E-03 4.4388294E-02 at 150iterations 1.1903653E-03 2.4355888E-02 at 160iterations 6.5409666E-04 1.3416290E-02 at 170iterations 3.6058633E-04 7.8315735E-03 at 180iterations finished qdiffx linear iterations at : 06:48:41 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 3.6058633E-04 7.8315735E-03 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 06:48:41 12.467u 0.205s 0:13.22 95.7% 0+0k 0+0io 0pf+0w