Tue Oct 11 04:20:41 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 Tue Oct 11 2011 at 04:20:42 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6651719 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): -14.75900 32.66100 ymin,ymax (A): 7.556000 55.78200 zmin,zma (A): 25.38800 78.90800 x,y,z range (A): 47.42000 48.22600 53.52000 scale (grids/A): 0.6651719 object centre (A): 8.951000 31.66900 52.14800 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.140018 assigned positive charge : 414.1557 centred at (gu) : 90.09800 90.46432 88.67815 assigned negative charge : -410.0164 centred at (gu) : 90.38382 90.26037 88.70679 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8148 nv = 96 ne = 84 npr = 56958 no. pairs analyzed = 56958 no. exposed pairs = 3279 no. arc points = 22474 no. surface atoms = 1102 nbur = 1648 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 463 mr = 4766 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2100000 number of dielectric boundary points 3789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2150 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4590802E-08 4.0223505E-09 midg,1,midg; midg,igrid,midg -3.4082465E-08 6.5533207E-08 1,midg,midg; igrid,midg,midg 7.6404035E-08 -5.9408094E-08 gauss-seidel spectral radius is 0.9882918 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 04:20:42 rms-change max change #iterations 0.1769115 26.29308 at 10iterations 1.9534029E-02 2.241409 at 20iterations 2.1346994E-03 0.2833405 at 30iterations 2.3761272E-04 3.3363342E-02 at 40iterations 2.7923354E-05 3.6659241E-03 at 50iterations finished qdiffx linear iterations at : 04:20:45 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.7923354E-05 3.6659241E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 04:20:45 3.352u 0.179s 0:03.98 88.4% 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 Oct 11 2011 at 04:20:46 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.995516 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): -14.75900 32.66100 ymin,ymax (A): 7.556000 55.78200 zmin,zma (A): 25.38800 78.90800 x,y,z range (A): 47.42000 48.22600 53.52000 scale (grids/A): 1.995516 object centre (A): 8.951000 31.66900 52.14800 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.140018 assigned positive charge : 414.1557 centred at (gu) : 90.29353 91.39239 86.03364 assigned negative charge : -410.0164 centred at (gu) : 91.15130 90.78080 86.12015 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22474 grid for indexing accessible points = 1.400000 m= 32685 mr = 62577 m= 5324 mr = 24781 m= 377 mr = 3415 m= 6 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1857 time to turn everything in is 0.4100000 number of dielectric boundary points 34608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20574 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) : 0.6651719 object centre at (A) : 8.951000 31.66900 52.14800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5315954E-02 -2.4348175E-02 midg,1,midg; midg,igrid,midg -1.8217696E-02 4.5893926E-02 1,midg,midg; igrid,midg,midg 8.3823457E-02 -2.5204653E-02 gauss-seidel spectral radius is 0.9987606 estimated iterations to convergence 225 setup time was (sec) 0.6300000 now iterating at: 04:20:46 rms-change max change #iterations 4.815357 198.6289 at 10iterations 2.353320 72.86349 at 20iterations 1.138670 37.63979 at 30iterations 0.5549706 16.56216 at 40iterations 0.2697883 9.048622 at 50iterations 0.1313917 3.943787 at 60iterations 6.4019419E-02 2.122599 at 70iterations 3.1105088E-02 0.9672470 at 80iterations 1.5140986E-02 0.4261069 at 90iterations 7.3693832E-03 0.2158184 at 100iterations 3.5858895E-03 0.1035938 at 110iterations 1.7467136E-03 4.5637131E-02 at 120iterations finished qdiffx linear iterations at : 04:20:53 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.7467136E-03 4.5637131E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 04:20:54 7.880u 0.210s 0:08.59 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 Tue Oct 11 2011 at 04:20:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.993273 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): -14.75900 32.66100 ymin,ymax (A): 7.556000 55.78200 zmin,zma (A): 25.38800 78.90800 x,y,z range (A): 47.42000 48.22600 53.52000 scale (grids/A): 2.993273 object centre (A): 8.951000 31.66900 52.14800 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.140018 assigned positive charge : 414.1557 centred at (gu) : 90.44012 92.08842 84.05046 assigned negative charge : -410.0164 centred at (gu) : 91.72699 91.17118 84.18020 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 201692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22474 grid for indexing accessible points = 1.400000 m= 105359 mr = 151083 m= 38798 mr = 87738 m= 9771 mr = 31728 m= 1587 mr = 7515 m= 133 mr = 1077 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 6043 time to turn everything in is 1.110000 number of dielectric boundary points 78130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20783 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) : 1.995516 object centre at (A) : 8.951000 31.66900 52.14800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3723668 -0.6262450 midg,1,midg; midg,igrid,midg -0.1780765 0.5080107 1,midg,midg; igrid,midg,midg 0.7051147 -0.2259203 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 1.350000 now iterating at: 04:20:56 rms-change max change #iterations 10.96565 384.5746 at 10iterations 6.447829 131.2524 at 20iterations 3.779594 75.55215 at 30iterations 2.217412 42.88587 at 40iterations 1.293771 23.62319 at 50iterations 0.7576455 14.08405 at 60iterations 0.4412731 9.169941 at 70iterations 0.2575528 4.335110 at 80iterations 0.1500436 2.515525 at 90iterations 8.7435268E-02 1.463850 at 100iterations 5.0951850E-02 0.8733330 at 110iterations 2.9580405E-02 0.5307446 at 120iterations 1.7302306E-02 0.2936353 at 130iterations 1.0088734E-02 0.1644411 at 140iterations 5.8979173E-03 9.4916344E-02 at 150iterations 3.4672820E-03 5.7453156E-02 at 160iterations 2.0497080E-03 3.7429810E-02 at 170iterations 1.2305743E-03 2.0736694E-02 at 180iterations finished qdiffx linear iterations at : 04:21:07 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 1.2305743E-03 2.0736694E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 04:21:08 12.801u 0.198s 0:13.35 97.3% 0+0k 0+0io 0pf+0w