Sat Oct 8 21:15:21 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 Sat Oct 8 2011 at 21:15:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 546 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6216603 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): -31.96200 17.30700 ymin,ymax (A): -23.54400 23.41800 zmin,zma (A): -12.42300 44.84300 x,y,z range (A): 49.26900 46.96200 57.26600 scale (grids/A): 0.6216603 object centre (A): -7.327500 -6.2999725E-02 16.21000 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.61728 88.96758 89.63634 assigned negative charge : -387.4045 centred at (gu) : 88.53020 89.02287 89.51611 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6475 nv = 96 ne = 84 npr = 54009 no. pairs analyzed = 54009 no. exposed pairs = 3016 no. arc points = 21242 no. surface atoms = 1006 nbur = 1583 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3652 m= 0 mr = 26 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.3400000 number of dielectric boundary points 3122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8155 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4259472E-09 1.0800267E-08 midg,1,midg; midg,igrid,midg 9.1378576E-09 -2.7705757E-10 1,midg,midg; igrid,midg,midg -3.6741066E-09 6.9935941E-09 gauss-seidel spectral radius is 0.9865935 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 21:15:22 rms-change max change #iterations 0.1262387 20.34919 at 10iterations 1.1985782E-02 1.913090 at 20iterations 1.0962649E-03 0.1612225 at 30iterations 1.0304010E-04 1.7583847E-02 at 40iterations 9.5381602E-06 1.3656616E-03 at 50iterations finished qdiffx linear iterations at : 21:15:26 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 9.5381602E-06 1.3656616E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 21:15:26 4.078u 0.252s 0:04.59 94.1% 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 8 2011 at 21:15:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 546 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.864981 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): -31.96200 17.30700 ymin,ymax (A): -23.54400 23.41800 zmin,zma (A): -12.42300 44.84300 x,y,z range (A): 49.26900 46.96200 57.26600 scale (grids/A): 1.864981 object centre (A): -7.327500 -6.2999725E-02 16.21000 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.85139 86.90249 88.90884 assigned negative charge : -387.4045 centred at (gu) : 85.59004 87.06838 88.54836 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21242 grid for indexing accessible points = 1.400000 m= 24110 mr = 50053 m= 3300 mr = 17735 m= 165 mr = 2007 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 5527 time to turn everything in is 0.6200000 number of dielectric boundary points 28822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19278 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) : 0.6216603 object centre at (A) : -7.327500 -6.2999725E-02 16.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3094336E-02 1.7932052E-02 midg,1,midg; midg,igrid,midg 1.6138563E-02 4.9159983E-03 1,midg,midg; igrid,midg,midg -3.7149691E-03 2.9192172E-02 gauss-seidel spectral radius is 0.9985723 estimated iterations to convergence 210 setup time was (sec) 0.9100000 now iterating at: 21:15:27 rms-change max change #iterations 4.049284 193.4707 at 10iterations 1.863386 68.36838 at 20iterations 0.8556442 27.41528 at 30iterations 0.3933226 12.15657 at 40iterations 0.1825505 6.706282 at 50iterations 8.3568551E-02 2.607445 at 60iterations 3.8587216E-02 1.263065 at 70iterations 1.7751653E-02 0.5805025 at 80iterations 8.1645036E-03 0.2669888 at 90iterations 3.7696222E-03 0.1172180 at 100iterations 1.7343315E-03 5.4046631E-02 at 110iterations 8.0081308E-04 2.4058342E-02 at 120iterations finished qdiffx linear iterations at : 21:15:36 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 8.0081308E-04 2.4058342E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 21:15:36 9.317u 0.305s 0:09.88 97.2% 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 Sat Oct 8 2011 at 21:15:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 546 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.797471 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): -31.96200 17.30700 ymin,ymax (A): -23.54400 23.41800 zmin,zma (A): -12.42300 44.84300 x,y,z range (A): 49.26900 46.96200 57.26600 scale (grids/A): 2.797471 object centre (A): -7.327500 -6.2999725E-02 16.21000 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.77695 85.35356 88.36301 assigned negative charge : -387.4045 centred at (gu) : 83.38507 85.60262 87.82236 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 164772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21242 grid for indexing accessible points = 1.400000 m= 80701 mr = 121019 m= 26562 mr = 66480 m= 5793 mr = 21274 m= 654 mr = 4311 m= 24 mr = 399 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 19198 time to turn everything in is 1.560000 number of dielectric boundary points 65014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19629 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) : 1.864981 object centre at (A) : -7.327500 -6.2999725E-02 16.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1733441 0.1774970 midg,1,midg; midg,igrid,midg 0.1778323 3.9947197E-02 1,midg,midg; igrid,midg,midg -2.1053856E-02 0.3561887 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.880000 now iterating at: 21:15:38 rms-change max change #iterations 9.438648 366.3983 at 10iterations 5.414373 144.6105 at 20iterations 3.092535 82.52049 at 30iterations 1.760823 40.22670 at 40iterations 1.004404 23.34447 at 50iterations 0.5703613 10.56444 at 60iterations 0.3250852 5.981136 at 70iterations 0.1845856 3.473589 at 80iterations 0.1053049 1.954498 at 90iterations 5.9625652E-02 1.294826 at 100iterations 3.3979315E-02 0.6671295 at 110iterations 1.9342070E-02 0.3650913 at 120iterations 1.0995150E-02 0.2325363 at 130iterations 6.2504476E-03 0.1289177 at 140iterations 3.5536406E-03 6.6926956E-02 at 150iterations 2.0135748E-03 3.7164450E-02 at 160iterations 1.1489507E-03 2.3012161E-02 at 170iterations 6.5077061E-04 1.3021469E-02 at 180iterations finished qdiffx linear iterations at : 21:15:52 total time elapsed so far: 15.26000 # loops : 180 mean,max change (kT/e) : 6.5077061E-04 1.3021469E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.43000 DelPhi exited at 21:15:52 15.436u 0.313s 0:16.02 98.2% 0+0k 0+0io 0pf+0w