Tue Oct 11 06:16:00 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 Tue Oct 11 2011 at 06:16:00 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7248295 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): -19.01400 24.18900 ymin,ymax (A): -12.00500 28.80800 zmin,zma (A): -3.058000 46.05700 x,y,z range (A): 43.20300 40.81300 49.11500 scale (grids/A): 0.7248295 object centre (A): 2.587500 8.401501 21.49950 number of atom coordinates read : 2003 total number of charged atoms : 1887 net assigned charge : 6.025006 assigned positive charge : 306.8332 centred at (gu) : 89.80339 89.76754 91.08020 assigned negative charge : -300.8081 centred at (gu) : 89.62080 89.80104 91.14629 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7234 nv = 96 ne = 84 npr = 39937 no. pairs analyzed = 39937 no. exposed pairs = 2467 no. arc points = 16748 no. surface atoms = 844 nbur = 1159 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4168 m= 5 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 3497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1576 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 7789 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0008181E-07 3.6565009E-08 midg,1,midg; midg,igrid,midg 1.0446675E-07 5.1260177E-08 1,midg,midg; igrid,midg,midg -5.4729238E-08 1.9413838E-07 gauss-seidel spectral radius is 0.9900677 estimated iterations to convergence 82 setup time was (sec) 0.3300000 now iterating at: 06:16:01 rms-change max change #iterations 0.2198899 34.48726 at 10iterations 2.8693449E-02 3.998166 at 20iterations 4.0210802E-03 0.5716171 at 30iterations 6.5169320E-04 9.0551376E-02 at 40iterations 1.5463651E-04 2.0118713E-02 at 50iterations finished qdiffx linear iterations at : 06:16:04 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.5463651E-04 2.0118713E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 06:16:04 3.284u 0.183s 0:03.98 86.9% 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 Tue Oct 11 2011 at 06:16:04 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.174489 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): -19.01400 24.18900 ymin,ymax (A): -12.00500 28.80800 zmin,zma (A): -3.058000 46.05700 x,y,z range (A): 43.20300 40.81300 49.11500 scale (grids/A): 2.174489 object centre (A): 2.587500 8.401501 21.49950 number of atom coordinates read : 2003 total number of charged atoms : 1887 net assigned charge : 6.025006 assigned positive charge : 306.8332 centred at (gu) : 89.41032 89.30289 93.24081 assigned negative charge : -300.8081 centred at (gu) : 88.86239 89.40327 93.43887 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16748 grid for indexing accessible points = 1.400000 m= 32082 mr = 54109 m= 6896 mr = 24684 m= 716 mr = 4642 m= 20 mr = 371 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 32152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15011 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) : 0.7248295 object centre at (A) : 2.587500 8.401501 21.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4948736E-02 1.0323462E-02 midg,1,midg; midg,igrid,midg 3.4129020E-02 7.7695488E-03 1,midg,midg; igrid,midg,midg 2.1135664E-02 5.5613924E-02 gauss-seidel spectral radius is 0.9988722 estimated iterations to convergence 236 setup time was (sec) 0.6100000 now iterating at: 06:16:05 rms-change max change #iterations 4.749554 174.3747 at 10iterations 2.383139 79.90656 at 20iterations 1.202223 37.93298 at 30iterations 0.6035302 17.60519 at 40iterations 0.3031982 9.929286 at 50iterations 0.1527126 4.508444 at 60iterations 7.6931603E-02 2.556091 at 70iterations 3.8756352E-02 1.160223 at 80iterations 1.9566165E-02 0.5724335 at 90iterations 9.9138133E-03 0.3139094 at 100iterations 5.0442512E-03 0.1370544 at 110iterations 2.6077311E-03 8.1153870E-02 at 120iterations finished qdiffx linear iterations at : 06:16:12 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.6077311E-03 8.1153870E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 06:16:13 7.701u 0.190s 0:08.39 94.0% 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 Tue Oct 11 2011 at 06:16:13 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.261733 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): -19.01400 24.18900 ymin,ymax (A): -12.00500 28.80800 zmin,zma (A): -3.058000 46.05700 x,y,z range (A): 43.20300 40.81300 49.11500 scale (grids/A): 3.261733 object centre (A): 2.587500 8.401501 21.49950 number of atom coordinates read : 2003 total number of charged atoms : 1887 net assigned charge : 6.025006 assigned positive charge : 306.8332 centred at (gu) : 89.11555 88.95446 94.86124 assigned negative charge : -300.8081 centred at (gu) : 88.29362 89.10497 95.15831 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16748 grid for indexing accessible points = 1.400000 m= 97785 mr = 129965 m= 42320 mr = 81705 m= 13206 mr = 35132 m= 2821 mr = 10354 m= 339 mr = 2046 m= 5 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 72505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15092 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) : 2.174489 object centre at (A) : 2.587500 8.401501 21.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1845082 3.0777875E-02 midg,1,midg; midg,igrid,midg 0.2564476 2.8465079E-02 1,midg,midg; igrid,midg,midg 0.4425082 0.4148700 gauss-seidel spectral radius is 0.9993058 estimated iterations to convergence 299 setup time was (sec) 1.420000 now iterating at: 06:16:14 rms-change max change #iterations 10.46667 290.0677 at 10iterations 6.230155 136.3679 at 20iterations 3.691751 75.60555 at 30iterations 2.186986 43.87980 at 40iterations 1.296694 23.59792 at 50iterations 0.7623714 13.63041 at 60iterations 0.4502692 7.942047 at 70iterations 0.2643395 4.562195 at 80iterations 0.1559541 2.517570 at 90iterations 9.1702662E-02 1.659805 at 100iterations 5.3996637E-02 0.8892410 at 110iterations 3.2029308E-02 0.5699883 at 120iterations 1.9096307E-02 0.3182716 at 130iterations 1.1556553E-02 0.2021751 at 140iterations 7.1876142E-03 0.1324539 at 150iterations 4.6401839E-03 9.0145111E-02 at 160iterations 3.1610499E-03 5.3754807E-02 at 170iterations 2.2936382E-03 4.0870667E-02 at 180iterations finished qdiffx linear iterations at : 06:16:26 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 2.2936382E-03 4.0870667E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 06:16:26 12.631u 0.196s 0:13.25 96.7% 0+0k 0+0io 0pf+0w