Tue Oct 11 04:23:03 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 04:23:03 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6722689 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): -15.28100 32.82100 ymin,ymax (A): 6.767000 55.08100 zmin,zma (A): 25.63800 78.59300 x,y,z range (A): 48.10200 48.31400 52.95500 scale (grids/A): 0.6722689 object centre (A): 8.770000 30.92400 52.11550 number of atom coordinates read : 2752 total number of charged atoms : 2600 net assigned charge : 3.176017 assigned positive charge : 418.0398 centred at (gu) : 90.22591 90.55556 88.68892 assigned negative charge : -414.8643 centred at (gu) : 90.54588 90.38939 88.63437 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8357 nv = 96 ne = 84 npr = 57029 no. pairs analyzed = 57029 no. exposed pairs = 3297 no. arc points = 23151 no. surface atoms = 1108 nbur = 1644 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4811 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.2100000 number of dielectric boundary points 3980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9747 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7986593E-09 2.0807905E-08 midg,1,midg; midg,igrid,midg -3.2932768E-08 6.5618110E-08 1,midg,midg; igrid,midg,midg 9.5903886E-08 -8.7644075E-08 gauss-seidel spectral radius is 0.9885398 estimated iterations to convergence 76 setup time was (sec) 0.4000000 now iterating at: 04:23:04 rms-change max change #iterations 0.1855181 21.75528 at 10iterations 2.0790700E-02 2.450745 at 20iterations 2.3215085E-03 0.3079987 at 30iterations 2.7352135E-04 3.3592224E-02 at 40iterations 3.6750469E-05 4.7149658E-03 at 50iterations finished qdiffx linear iterations at : 04:23:06 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.6750469E-05 4.7149658E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 04:23:07 3.360u 0.162s 0:04.09 86.0% 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 04:23:07 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.016807 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): -15.28100 32.82100 ymin,ymax (A): 6.767000 55.08100 zmin,zma (A): 25.63800 78.59300 x,y,z range (A): 48.10200 48.31400 52.95500 scale (grids/A): 2.016807 object centre (A): 8.770000 30.92400 52.11550 number of atom coordinates read : 2752 total number of charged atoms : 2600 net assigned charge : 3.176017 assigned positive charge : 418.0398 centred at (gu) : 90.67716 91.66589 86.06654 assigned negative charge : -414.8643 centred at (gu) : 91.63738 91.16801 85.90289 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 89182 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23151 grid for indexing accessible points = 1.400000 m= 34806 mr = 63420 m= 6246 mr = 26440 m= 462 mr = 4097 m= 11 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1577 time to turn everything in is 0.4300000 number of dielectric boundary points 36521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20544 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) : 0.6722689 object centre at (A) : 8.770000 30.92400 52.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5373369E-02 1.4023272E-02 midg,1,midg; midg,igrid,midg -1.7576270E-02 4.7560912E-02 1,midg,midg; igrid,midg,midg 9.0590790E-02 -3.0347029E-02 gauss-seidel spectral radius is 0.9987872 estimated iterations to convergence 227 setup time was (sec) 0.6500000 now iterating at: 04:23:08 rms-change max change #iterations 4.920101 197.7579 at 10iterations 2.417229 72.47217 at 20iterations 1.179910 38.84047 at 30iterations 0.5801063 19.75490 at 40iterations 0.2843280 8.853518 at 50iterations 0.1392372 4.076874 at 60iterations 6.8349756E-02 1.873043 at 70iterations 3.3529405E-02 0.9371563 at 80iterations 1.6400173E-02 0.4488487 at 90iterations 8.0511151E-03 0.2186534 at 100iterations 3.9411685E-03 0.1134815 at 110iterations 1.9343265E-03 5.5006027E-02 at 120iterations finished qdiffx linear iterations at : 04:23:15 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.9343265E-03 5.5006027E-02 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 04:23:15 7.808u 0.197s 0:08.30 96.2% 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 04:23:15 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 3.025210 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): -15.28100 32.82100 ymin,ymax (A): 6.767000 55.08100 zmin,zma (A): 25.63800 78.59300 x,y,z range (A): 48.10200 48.31400 52.95500 scale (grids/A): 3.025210 object centre (A): 8.770000 30.92400 52.11550 number of atom coordinates read : 2752 total number of charged atoms : 2600 net assigned charge : 3.176017 assigned positive charge : 418.0398 centred at (gu) : 91.01573 92.49870 84.09975 assigned negative charge : -414.8643 centred at (gu) : 92.45596 91.75188 83.85433 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 206114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23151 grid for indexing accessible points = 1.400000 m= 109477 mr = 153077 m= 43343 mr = 91025 m= 11533 mr = 35728 m= 1933 mr = 8967 m= 196 mr = 1295 m= 7 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 5205 time to turn everything in is 1.140000 number of dielectric boundary points 82375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 20789 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) : 2.016807 object centre at (A) : 8.770000 30.92400 52.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8912437E-02 7.0548423E-02 midg,1,midg; midg,igrid,midg -0.1777680 0.5316451 1,midg,midg; igrid,midg,midg 0.7264768 -0.1648835 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 1.370000 now iterating at: 04:23:17 rms-change max change #iterations 11.24449 470.4065 at 10iterations 6.635511 156.2030 at 20iterations 3.906149 88.63131 at 30iterations 2.299376 40.49882 at 40iterations 1.348076 22.32137 at 50iterations 0.7909158 14.32438 at 60iterations 0.4630325 9.203567 at 70iterations 0.2716189 4.664680 at 80iterations 0.1586982 2.654961 at 90iterations 9.2742339E-02 1.733257 at 100iterations 5.4153282E-02 0.9320221 at 110iterations 3.1637020E-02 0.5158195 at 120iterations 1.8452721E-02 0.3092413 at 130iterations 1.0785173E-02 0.1863003 at 140iterations 6.3121072E-03 9.9512100E-02 at 150iterations 3.6999055E-03 6.5063477E-02 at 160iterations 2.1790408E-03 3.5715103E-02 at 170iterations 1.2865944E-03 2.3223877E-02 at 180iterations finished qdiffx linear iterations at : 04:23:28 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.2865944E-03 2.3223877E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 04:23:29 12.859u 0.223s 0:13.43 97.3% 0+0k 0+0io 0pf+0w