Sat Oct 8 13:46:56 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 Sat Oct 8 2011 at 13:46:56 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6347395 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): -12.02900 42.29300 ymin,ymax (A): -22.73800 22.44600 zmin,zma (A): -7.932000 48.15400 x,y,z range (A): 54.32200 45.18400 56.08600 scale (grids/A): 0.6347395 object centre (A): 15.13200 -0.1459999 20.11100 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 1.4008060E-02 assigned positive charge : 457.1326 centred at (gu) : 89.16734 89.72699 91.59322 assigned negative charge : -457.1193 centred at (gu) : 89.15225 89.63462 91.51608 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8075 nv = 96 ne = 84 npr = 63653 no. pairs analyzed = 63653 no. exposed pairs = 3430 no. arc points = 23956 no. surface atoms = 1167 nbur = 1873 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 418 mr = 4733 m= 4 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 3717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2385 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9912 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5780785E-09 1.2789176E-08 midg,1,midg; midg,igrid,midg -1.1839412E-08 1.0126612E-08 1,midg,midg; igrid,midg,midg -2.2589723E-09 1.4161271E-09 gauss-seidel spectral radius is 0.9871731 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 13:46:57 rms-change max change #iterations 0.1537929 24.51414 at 10iterations 1.5520133E-02 1.886387 at 20iterations 1.5351918E-03 0.2022800 at 30iterations 1.7491505E-04 2.2750854E-02 at 40iterations 2.4736028E-05 3.1776428E-03 at 50iterations finished qdiffx linear iterations at : 13:47:01 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 2.4736028E-05 3.1776428E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 13:47:01 4.459u 0.415s 0:05.21 93.2% 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 13:47:01 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.904218 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): -12.02900 42.29300 ymin,ymax (A): -22.73800 22.44600 zmin,zma (A): -7.932000 48.15400 x,y,z range (A): 54.32200 45.18400 56.08600 scale (grids/A): 1.904218 object centre (A): 15.13200 -0.1459999 20.11100 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 1.4008060E-02 assigned positive charge : 457.1326 centred at (gu) : 87.50153 89.18014 94.77922 assigned negative charge : -457.1193 centred at (gu) : 87.45671 88.90369 94.54813 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23956 grid for indexing accessible points = 1.400000 m= 31933 mr = 64290 m= 4587 mr = 23951 m= 244 mr = 2780 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 22767 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) : 0.6347395 object centre at (A) : 15.13200 -0.1459999 20.11100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6685592E-02 1.9968430E-02 midg,1,midg; midg,igrid,midg -2.9687907E-03 1.8774044E-02 1,midg,midg; igrid,midg,midg -3.3095516E-02 9.9104876E-03 gauss-seidel spectral radius is 0.9986692 estimated iterations to convergence 217 setup time was (sec) 0.9800000 now iterating at: 13:47:03 rms-change max change #iterations 4.670746 182.1794 at 10iterations 2.218228 63.80538 at 20iterations 1.050106 31.45774 at 30iterations 0.4965293 14.37554 at 40iterations 0.2360294 6.970984 at 50iterations 0.1116384 3.298019 at 60iterations 5.2829299E-02 1.476984 at 70iterations 2.4996284E-02 0.7427379 at 80iterations 1.1879054E-02 0.3434391 at 90iterations 5.6154500E-03 0.1755371 at 100iterations 2.6670855E-03 8.5075378E-02 at 110iterations 1.2652527E-03 3.5868645E-02 at 120iterations finished qdiffx linear iterations at : 13:47:12 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 1.2652527E-03 3.5868645E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.57000 DelPhi exited at 13:47:13 10.579u 0.455s 0:11.54 95.4% 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 Sat Oct 8 2011 at 13:47:13 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.856328 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): -12.02900 42.29300 ymin,ymax (A): -22.73800 22.44600 zmin,zma (A): -7.932000 48.15400 x,y,z range (A): 54.32200 45.18400 56.08600 scale (grids/A): 2.856328 object centre (A): 15.13200 -0.1459999 20.11100 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 1.4008060E-02 assigned positive charge : 457.1326 centred at (gu) : 86.25220 88.77014 97.16875 assigned negative charge : -457.1193 centred at (gu) : 86.18502 88.35559 96.82195 start vw surface at 0.1400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 205365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23956 grid for indexing accessible points = 1.400000 m= 105254 mr = 155263 m= 36096 mr = 87655 m= 8062 mr = 29171 m= 1105 mr = 5855 m= 52 mr = 699 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 77286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 23139 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) : 1.904218 object centre at (A) : 15.13200 -0.1459999 20.11100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4709613E-02 0.3765417 midg,1,midg; midg,igrid,midg -3.0213278E-02 0.2369428 1,midg,midg; igrid,midg,midg -0.4986999 0.1783533 gauss-seidel spectral radius is 0.9992708 estimated iterations to convergence 292 setup time was (sec) 2.180000 now iterating at: 13:47:16 rms-change max change #iterations 10.85800 395.7700 at 10iterations 6.368493 134.6690 at 20iterations 3.706918 82.76045 at 30iterations 2.154437 38.90641 at 40iterations 1.253306 22.78169 at 50iterations 0.7259822 14.94584 at 60iterations 0.4211982 7.293896 at 70iterations 0.2434110 4.267311 at 80iterations 0.1412777 2.312704 at 90iterations 8.1485830E-02 1.531681 at 100iterations 4.7111575E-02 0.7451906 at 110iterations 2.7223431E-02 0.4605865 at 120iterations 1.5757475E-02 0.2656379 at 130iterations 9.1189276E-03 0.1523037 at 140iterations 5.2538514E-03 8.2000732E-02 at 150iterations 3.0443871E-03 4.9846172E-02 at 160iterations 1.7671972E-03 2.8440475E-02 at 170iterations 1.0260374E-03 1.8595219E-02 at 180iterations finished qdiffx linear iterations at : 13:47:33 total time elapsed so far: 19.61000 # loops : 180 mean,max change (kT/e) : 1.0260374E-03 1.8595219E-02 energy calculations done at 19.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.79000 DelPhi exited at 13:47:34 19.794u 0.470s 0:20.57 98.4% 0+0k 0+0io 0pf+0w