Sat Oct 8 14:26:40 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 14:26:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! 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: 0.6109071 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): -22.80100 26.79400 ymin,ymax (A): -24.08500 26.87000 zmin,zma (A): -22.82200 35.45200 x,y,z range (A): 49.59500 50.95500 58.27400 scale (grids/A): 0.6109071 object centre (A): 1.996500 1.392500 6.315000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4936 centred at (gu) : 88.50251 89.06363 87.13663 assigned negative charge : -453.4943 centred at (gu) : 88.45245 89.01987 87.23637 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7388 nv = 96 ne = 84 npr = 64351 no. pairs analyzed = 64351 no. exposed pairs = 3427 no. arc points = 23973 no. surface atoms = 1173 nbur = 1858 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 4262 m= 0 mr = 19 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2445 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9284 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1012436E-08 -3.1745253E-09 midg,1,midg; midg,igrid,midg -3.3279874E-09 1.9791122E-09 1,midg,midg; igrid,midg,midg -4.3164583E-09 2.0066151E-09 gauss-seidel spectral radius is 0.9861558 estimated iterations to convergence 70 setup time was (sec) 0.6700000 now iterating at: 14:26:41 rms-change max change #iterations 0.1292520 17.58980 at 10iterations 1.1760540E-02 1.725216 at 20iterations 1.2027393E-03 0.1812782 at 30iterations 1.5794030E-04 2.3307800E-02 at 40iterations 2.9896442E-05 4.9705505E-03 at 50iterations finished qdiffx linear iterations at : 14:26:46 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 2.9896442E-05 4.9705505E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 14:26:46 5.300u 0.485s 0:06.12 94.4% 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 14:26:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! 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: 1.832721 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): -22.80100 26.79400 ymin,ymax (A): -24.08500 26.87000 zmin,zma (A): -22.82200 35.45200 x,y,z range (A): 49.59500 50.95500 58.27400 scale (grids/A): 1.832721 object centre (A): 1.996500 1.392500 6.315000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4936 centred at (gu) : 85.50699 87.19043 81.40916 assigned negative charge : -453.4943 centred at (gu) : 85.35694 87.05939 81.70892 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 28157 mr = 58231 m= 3725 mr = 21001 m= 161 mr = 2205 m= 0 mr = 47 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 558 time to turn everything in is 0.6800000 number of dielectric boundary points 31520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22593 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) : 0.6109071 object centre at (A) : 1.996500 1.392500 6.315000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5893215E-02 -2.1074370E-02 midg,1,midg; midg,igrid,midg 1.4897614E-03 1.4105014E-02 1,midg,midg; igrid,midg,midg -8.9383246E-03 3.8915062E-03 gauss-seidel spectral radius is 0.9985586 estimated iterations to convergence 209 setup time was (sec) 1.030000 now iterating at: 14:26:48 rms-change max change #iterations 4.294703 174.0854 at 10iterations 1.974636 63.40135 at 20iterations 0.9082791 26.84635 at 30iterations 0.4179504 14.28926 at 40iterations 0.1920608 6.294575 at 50iterations 8.8321783E-02 2.799263 at 60iterations 4.0442072E-02 1.377766 at 70iterations 1.8644297E-02 0.5633106 at 80iterations 8.5990131E-03 0.2631607 at 90iterations 3.9536189E-03 0.1183107 at 100iterations 1.8188949E-03 5.6129456E-02 at 110iterations 8.3841174E-04 2.9750824E-02 at 120iterations finished qdiffx linear iterations at : 14:26:59 total time elapsed so far: 12.41000 # loops : 120 mean,max change (kT/e) : 8.3841174E-04 2.9750824E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 14:27:00 12.585u 0.535s 0:13.46 97.3% 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 14:27:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! 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: 2.749082 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): -22.80100 26.79400 ymin,ymax (A): -24.08500 26.87000 zmin,zma (A): -22.82200 35.45200 x,y,z range (A): 49.59500 50.95500 58.27400 scale (grids/A): 2.749082 object centre (A): 1.996500 1.392500 6.315000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4936 centred at (gu) : 83.26033 85.78529 77.11366 assigned negative charge : -453.4943 centred at (gu) : 83.03539 85.58889 77.56335 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 187703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23973 grid for indexing accessible points = 1.400000 m= 94141 mr = 140937 m= 31278 mr = 78136 m= 6331 mr = 25040 m= 690 mr = 4627 m= 16 mr = 386 m= 0 mr = 4 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1856 time to turn everything in is 1.730000 number of dielectric boundary points 71029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 23071 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) : 1.832721 object centre at (A) : 1.996500 1.392500 6.315000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6542878 -0.1659875 midg,1,midg; midg,igrid,midg 9.4029762E-02 0.1595971 1,midg,midg; igrid,midg,midg -5.2558728E-02 3.5949696E-02 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 2.120000 now iterating at: 14:27:02 rms-change max change #iterations 10.16590 267.8443 at 10iterations 5.886376 124.6570 at 20iterations 3.399400 67.43536 at 30iterations 1.950650 37.79475 at 40iterations 1.117517 22.82123 at 50iterations 0.6390822 11.35297 at 60iterations 0.3653885 6.826698 at 70iterations 0.2091966 3.801861 at 80iterations 0.1195219 2.062965 at 90iterations 6.8305053E-02 1.225231 at 100iterations 3.9025575E-02 0.6599886 at 110iterations 2.2241542E-02 0.3863602 at 120iterations 1.2721138E-02 0.2336411 at 130iterations 7.2643361E-03 0.1194153 at 140iterations 4.1470551E-03 6.8407059E-02 at 150iterations 2.3732008E-03 4.3113708E-02 at 160iterations 1.3561571E-03 2.4809837E-02 at 170iterations 7.7662669E-04 1.3610840E-02 at 180iterations finished qdiffx linear iterations at : 14:27:24 total time elapsed so far: 23.92000 # loops : 180 mean,max change (kT/e) : 7.7662669E-04 1.3610840E-02 energy calculations done at 23.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.10000 DelPhi exited at 14:27:25 24.100u 0.601s 0:24.97 98.9% 0+0k 0+0io 0pf+0w