Sat Oct 15 13:38:25 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 15 2011 at 13:38:25 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2158 !!! WARNING: ASL 36 has a net charge of -0.1000 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: 0.6904711 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): -22.27800 24.56100 ymin,ymax (A): -54.56800 -9.044000 zmin,zma (A): -32.57900 18.98000 x,y,z range (A): 46.83900 45.52400 51.55900 scale (grids/A): 0.6904711 object centre (A): 1.141500 -31.80600 -6.799501 number of atom coordinates read : 2158 total number of charged atoms : 2018 net assigned charge : -6.099980 assigned positive charge : 326.8987 centred at (gu) : 89.29907 90.75406 91.41499 assigned negative charge : -332.9988 centred at (gu) : 89.33683 90.81860 91.60030 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7081 nv = 96 ne = 84 npr = 43217 no. pairs analyzed = 43217 no. exposed pairs = 2838 no. arc points = 20145 no. surface atoms = 955 nbur = 1203 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 3822 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.1800000 number of dielectric boundary points 3671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1783 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3680780E-08 -1.3335230E-07 midg,1,midg; midg,igrid,midg -8.7821483E-09 -6.5003036E-08 1,midg,midg; igrid,midg,midg -2.2060036E-08 -4.0430702E-08 gauss-seidel spectral radius is 0.9890895 estimated iterations to convergence 78 setup time was (sec) 0.4400000 now iterating at: 13:38:26 rms-change max change #iterations 0.1921921 27.88897 at 10iterations 2.2489168E-02 2.873365 at 20iterations 2.6116471E-03 0.3704224 at 30iterations 3.0449536E-04 4.0594101E-02 at 40iterations 3.5667981E-05 4.6174526E-03 at 50iterations finished qdiffx linear iterations at : 13:38:31 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 3.5667981E-05 4.6174526E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 13:38:32 3.748u 0.287s 0:06.69 60.0% 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 15 2011 at 13:38:33 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2158 !!! WARNING: ASL 36 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.071413 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): -22.27800 24.56100 ymin,ymax (A): -54.56800 -9.044000 zmin,zma (A): -32.57900 18.98000 x,y,z range (A): 46.83900 45.52400 51.55900 scale (grids/A): 2.071413 object centre (A): 1.141500 -31.80600 -6.799501 number of atom coordinates read : 2158 total number of charged atoms : 2018 net assigned charge : -6.099980 assigned positive charge : 326.8987 centred at (gu) : 87.89695 92.26192 94.24480 assigned negative charge : -332.9988 centred at (gu) : 88.01048 92.45557 94.80077 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20145 grid for indexing accessible points = 1.400000 m= 28728 mr = 50786 m= 5662 mr = 21410 m= 473 mr = 3842 m= 8 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1242 time to turn everything in is 0.3900000 number of dielectric boundary points 33643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 16021 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) : 0.6904711 object centre at (A) : 1.141500 -31.80600 -6.799501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6261261E-02 -0.1281187 midg,1,midg; midg,igrid,midg -1.6826456E-02 -3.2151572E-02 1,midg,midg; igrid,midg,midg 6.2802527E-03 -2.3504435E-03 gauss-seidel spectral radius is 0.9987992 estimated iterations to convergence 228 setup time was (sec) 0.6400000 now iterating at: 13:38:34 rms-change max change #iterations 4.617641 197.5450 at 10iterations 2.254708 88.01981 at 20iterations 1.103745 35.78579 at 30iterations 0.5394819 16.56393 at 40iterations 0.2651794 7.821534 at 50iterations 0.1295196 3.817156 at 60iterations 6.3817225E-02 1.978819 at 70iterations 3.1218762E-02 1.118238 at 80iterations 1.5337721E-02 0.5215940 at 90iterations 7.4947453E-03 0.2435493 at 100iterations 3.6746559E-03 0.1052103 at 110iterations 1.8043852E-03 5.7601929E-02 at 120iterations finished qdiffx linear iterations at : 13:38:44 total time elapsed so far: 8.920000 # loops : 120 mean,max change (kT/e) : 1.8043852E-03 5.7601929E-02 energy calculations done at 8.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 13:38:45 9.047u 0.270s 0:12.30 75.6% 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 15 2011 at 13:38:45 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2158 !!! WARNING: ASL 36 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.107120 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): -22.27800 24.56100 ymin,ymax (A): -54.56800 -9.044000 zmin,zma (A): -32.57900 18.98000 x,y,z range (A): 46.83900 45.52400 51.55900 scale (grids/A): 3.107120 object centre (A): 1.141500 -31.80600 -6.799501 number of atom coordinates read : 2158 total number of charged atoms : 2018 net assigned charge : -6.099980 assigned positive charge : 326.8987 centred at (gu) : 86.84544 93.39287 96.36715 assigned negative charge : -332.9988 centred at (gu) : 87.01563 93.68340 97.20097 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 173095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20145 grid for indexing accessible points = 1.400000 m= 89395 mr = 123031 m= 36313 mr = 73115 m= 10495 mr = 29607 m= 2026 mr = 8303 m= 173 mr = 1496 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 4202 time to turn everything in is 1.220000 number of dielectric boundary points 75859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 16144 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) : 2.071413 object centre at (A) : 1.141500 -31.80600 -6.799501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2552328 -1.313365 midg,1,midg; midg,igrid,midg -0.1571175 -0.2254883 1,midg,midg; igrid,midg,midg 7.4177943E-02 -5.0144978E-02 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 1.510000 now iterating at: 13:38:47 rms-change max change #iterations 10.29274 534.0797 at 10iterations 6.022737 145.3759 at 20iterations 3.510955 72.76968 at 30iterations 2.043644 40.58798 at 40iterations 1.191827 21.32744 at 50iterations 0.6937228 15.61990 at 60iterations 0.4036059 7.718457 at 70iterations 0.2347307 4.554337 at 80iterations 0.1365064 2.294077 at 90iterations 7.9506241E-02 1.353636 at 100iterations 4.6123233E-02 0.8256421 at 110iterations 2.6817763E-02 0.4991856 at 120iterations 1.5582641E-02 0.2833786 at 130iterations 9.0758009E-03 0.1666379 at 140iterations 5.2541876E-03 0.1000391 at 150iterations 3.0602242E-03 5.5311203E-02 at 160iterations 1.7752078E-03 3.1333923E-02 at 170iterations 1.0342355E-03 1.8117905E-02 at 180iterations finished qdiffx linear iterations at : 13:39:03 total time elapsed so far: 15.96000 # loops : 180 mean,max change (kT/e) : 1.0342355E-03 1.8117905E-02 energy calculations done at 15.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.09000 DelPhi exited at 13:39:04 16.093u 0.314s 0:18.63 88.0% 0+0k 0+0io 0pf+0w