Tue Nov 22 14:12:44 PST 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 Nov 22 2011 at 14:12:48 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.5858057 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): -25.52800 35.24300 ymin,ymax (A): -18.88200 20.72100 zmin,zma (A): -3.423000 38.44600 x,y,z range (A): 60.77100 39.60300 41.86900 scale (grids/A): 0.5858057 object centre (A): 4.857500 0.9194994 17.51150 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 89.99590 90.19283 90.56147 assigned negative charge : -288.8263 centred at (gu) : 90.01798 90.26315 90.67445 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4519 nv = 96 ne = 84 npr = 40465 no. pairs analyzed = 40465 no. exposed pairs = 2453 no. arc points = 17330 no. surface atoms = 832 nbur = 1132 mkacc time = 8.0000006E-02 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 = 1.484000 m= 187 mr = 2404 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2200000 number of dielectric boundary points 2287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1810 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4119917E-09 -1.3368482E-09 midg,1,midg; midg,igrid,midg 1.9364432E-09 -4.3091566E-10 1,midg,midg; igrid,midg,midg 1.2000583E-09 4.3381426E-10 gauss-seidel spectral radius is 0.9848719 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 14:12:52 rms-change max change #iterations 8.5787423E-02 16.27911 at 10iterations 6.8556997E-03 1.309582 at 20iterations 5.5046682E-04 9.8814964E-02 at 30iterations 4.2915908E-05 9.9468231E-03 at 40iterations 3.4496413E-06 6.2942505E-04 at 50iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 3.4496413E-06 6.2942505E-04 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:13:05 3.067u 0.130s 0:17.30 18.4% 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 Nov 22 2011 at 14:13:07 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.757417 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): -25.52800 35.24300 ymin,ymax (A): -18.88200 20.72100 zmin,zma (A): -3.423000 38.44600 x,y,z range (A): 60.77100 39.60300 41.86900 scale (grids/A): 1.757417 object centre (A): 4.857500 0.9194994 17.51150 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 89.98754 90.57830 91.68438 assigned negative charge : -288.8263 centred at (gu) : 90.05412 90.78961 92.02351 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 48923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17330 grid for indexing accessible points = 1.400000 m= 16705 mr = 33169 m= 1990 mr = 12453 m= 60 mr = 1139 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1589 time to turn everything in is 0.3500000 number of dielectric boundary points 20894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14239 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) : 0.5858057 object centre at (A) : 4.857500 0.9194994 17.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1490196E-03 -4.9838396E-03 midg,1,midg; midg,igrid,midg 2.7295665E-03 -1.1817381E-03 1,midg,midg; igrid,midg,midg 3.4249350E-02 2.2219228E-02 gauss-seidel spectral radius is 0.9983206 estimated iterations to convergence 194 setup time was (sec) 0.6300000 now iterating at: 14:13:11 rms-change max change #iterations 3.105304 175.8968 at 10iterations 1.333395 56.38412 at 20iterations 0.5743721 25.11388 at 30iterations 0.2472343 11.15240 at 40iterations 0.1062609 4.375112 at 50iterations 4.5912866E-02 1.799386 at 60iterations 1.9775854E-02 0.8076959 at 70iterations 8.5049057E-03 0.3350983 at 80iterations 3.6609180E-03 0.1572476 at 90iterations 1.5779195E-03 6.3305855E-02 at 100iterations 6.7975483E-04 2.6739120E-02 at 110iterations 2.9424651E-04 1.1341095E-02 at 120iterations finished qdiffx linear iterations at : 14:13:30 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.9424651E-04 1.1341095E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 14:13:34 7.063u 0.188s 0:28.08 25.7% 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 Nov 22 2011 at 14:13:37 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.636126 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): -25.52800 35.24300 ymin,ymax (A): -18.88200 20.72100 zmin,zma (A): -3.423000 38.44600 x,y,z range (A): 60.77100 39.60300 41.86900 scale (grids/A): 2.636126 object centre (A): 4.857500 0.9194994 17.51150 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 89.98133 90.86755 92.52661 assigned negative charge : -288.8263 centred at (gu) : 90.08121 91.18446 93.03529 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 113158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17330 grid for indexing accessible points = 1.400000 m= 55979 mr = 80578 m= 18302 mr = 46090 m= 3216 mr = 14672 m= 243 mr = 2311 m= 9 mr = 148 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 5477 time to turn everything in is 0.8300000 number of dielectric boundary points 47106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14648 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) : 1.757417 object centre at (A) : 4.857500 0.9194994 17.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9526358E-02 -4.9245909E-02 midg,1,midg; midg,igrid,midg 2.3440385E-02 -7.3363422E-03 1,midg,midg; igrid,midg,midg 0.4026797 0.2438431 gauss-seidel spectral radius is 0.9991500 estimated iterations to convergence 271 setup time was (sec) 1.110000 now iterating at: 14:13:43 rms-change max change #iterations 7.563250 267.4401 at 10iterations 4.211598 121.9171 at 20iterations 2.340040 55.98056 at 30iterations 1.291570 30.36002 at 40iterations 0.7127647 16.72392 at 50iterations 0.3920473 9.173390 at 60iterations 0.2156873 5.009735 at 70iterations 0.1187844 2.671381 at 80iterations 6.5280668E-02 1.492407 at 90iterations 3.6018547E-02 0.8630219 at 100iterations 1.9834949E-02 0.4532466 at 110iterations 1.0952803E-02 0.2483130 at 120iterations 6.0218256E-03 0.1453147 at 130iterations 3.3050044E-03 7.3241711E-02 at 140iterations 1.8231472E-03 4.3071747E-02 at 150iterations 1.0034251E-03 2.5901794E-02 at 160iterations 5.5213924E-04 1.2584686E-02 at 170iterations 3.0351765E-04 7.5817108E-03 at 180iterations finished qdiffx linear iterations at : 14:14:13 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 3.0351765E-04 7.5817108E-03 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 14:14:19 11.321u 0.191s 0:42.80 26.8% 0+0k 0+0io 0pf+0w