Sat Oct 8 19:32:50 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 19:32:50 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 = 2567 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 344 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: 0.6291753 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): -31.88800 17.47600 ymin,ymax (A): -23.38000 24.31100 zmin,zma (A): -12.20600 44.37600 x,y,z range (A): 49.36400 47.69100 56.58200 scale (grids/A): 0.6291753 object centre (A): -7.206000 0.4654999 16.08500 number of atom coordinates read : 2567 total number of charged atoms : 2441 net assigned charge : 3.300009 assigned positive charge : 390.0051 centred at (gu) : 88.48989 88.74958 89.87901 assigned negative charge : -386.7055 centred at (gu) : 88.43482 88.81129 89.73402 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6707 nv = 96 ne = 84 npr = 53070 no. pairs analyzed = 53070 no. exposed pairs = 3020 no. arc points = 21506 no. surface atoms = 1022 nbur = 1545 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 323 mr = 3725 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.3000000 number of dielectric boundary points 3273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2179 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3658379E-09 1.5349238E-08 midg,1,midg; midg,igrid,midg 1.1539502E-08 -1.3309960E-09 1,midg,midg; igrid,midg,midg -1.8097761E-09 5.9431149E-09 gauss-seidel spectral radius is 0.9869103 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 19:32:50 rms-change max change #iterations 0.1377249 21.82919 at 10iterations 1.3394980E-02 2.112717 at 20iterations 1.2700759E-03 0.1867027 at 30iterations 1.2413293E-04 1.7562866E-02 at 40iterations 1.2425780E-05 1.7852783E-03 at 50iterations finished qdiffx linear iterations at : 19:32:53 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.2425780E-05 1.7852783E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 19:32:54 3.558u 0.235s 0:04.06 93.1% 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 19:32:54 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 344 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.887526 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): -31.88800 17.47600 ymin,ymax (A): -23.38000 24.31100 zmin,zma (A): -12.20600 44.37600 x,y,z range (A): 49.36400 47.69100 56.58200 scale (grids/A): 1.887526 object centre (A): -7.206000 0.4654999 16.08500 number of atom coordinates read : 2567 total number of charged atoms : 2441 net assigned charge : 3.300009 assigned positive charge : 390.0051 centred at (gu) : 85.46911 86.24810 89.63640 assigned negative charge : -386.7055 centred at (gu) : 85.30426 86.43351 89.20180 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21506 grid for indexing accessible points = 1.400000 m= 26243 mr = 50535 m= 3846 mr = 19583 m= 167 mr = 2278 m= 5 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2858 time to turn everything in is 0.5500000 number of dielectric boundary points 30150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19209 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) : 0.6291753 object centre at (A) : -7.206000 0.4654999 16.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2641327E-02 2.5074728E-02 midg,1,midg; midg,igrid,midg 1.7883252E-02 1.6904010E-03 1,midg,midg; igrid,midg,midg -1.0850345E-03 2.8576266E-02 gauss-seidel spectral radius is 0.9986055 estimated iterations to convergence 212 setup time was (sec) 0.8600000 now iterating at: 19:32:55 rms-change max change #iterations 4.146101 177.4121 at 10iterations 1.928227 68.46160 at 20iterations 0.8946764 34.05164 at 30iterations 0.4144424 13.57721 at 40iterations 0.1927493 6.902374 at 50iterations 8.9842930E-02 2.839417 at 60iterations 4.1716658E-02 1.266294 at 70iterations 1.9456336E-02 0.6238365 at 80iterations 9.0265647E-03 0.3107384 at 90iterations 4.1881250E-03 0.1353760 at 100iterations 1.9484917E-03 5.9799194E-02 at 110iterations 9.0560166E-04 2.7374268E-02 at 120iterations finished qdiffx linear iterations at : 19:33:02 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 9.0560166E-04 2.7374268E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 19:33:02 8.153u 0.266s 0:08.68 96.8% 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 19:33:02 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 = 2567 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 344 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: 2.831289 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): -31.88800 17.47600 ymin,ymax (A): -23.38000 24.31100 zmin,zma (A): -12.20600 44.37600 x,y,z range (A): 49.36400 47.69100 56.58200 scale (grids/A): 2.831289 object centre (A): -7.206000 0.4654999 16.08500 number of atom coordinates read : 2567 total number of charged atoms : 2441 net assigned charge : 3.300009 assigned positive charge : 390.0051 centred at (gu) : 83.20350 84.37218 89.45456 assigned negative charge : -386.7055 centred at (gu) : 82.95633 84.65012 88.80257 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167287 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21506 grid for indexing accessible points = 1.400000 m= 85235 mr = 122200 m= 30512 mr = 70489 m= 6591 mr = 24539 m= 791 mr = 4885 m= 44 mr = 485 m= 0 mr = 13 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 9833 time to turn everything in is 1.330000 number of dielectric boundary points 67849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 19526 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) : 1.887526 object centre at (A) : -7.206000 0.4654999 16.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1667618E-02 0.2687850 midg,1,midg; midg,igrid,midg 0.1934875 3.6483057E-02 1,midg,midg; igrid,midg,midg 1.9830652E-02 0.3394992 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.670000 now iterating at: 19:33:04 rms-change max change #iterations 9.669917 352.6500 at 10iterations 5.573823 211.3562 at 20iterations 3.188112 67.82584 at 30iterations 1.825082 34.55548 at 40iterations 1.043859 21.29222 at 50iterations 0.5971183 11.58078 at 60iterations 0.3417559 6.229021 at 70iterations 0.1949449 3.868200 at 80iterations 0.1112839 2.277851 at 90iterations 6.3495241E-02 1.225174 at 100iterations 3.6359109E-02 0.6474895 at 110iterations 2.0736733E-02 0.4174118 at 120iterations 1.1837963E-02 0.2406883 at 130iterations 6.7670597E-03 0.1282425 at 140iterations 3.8633291E-03 7.6192856E-02 at 150iterations 2.2040405E-03 4.5429230E-02 at 160iterations 1.2604735E-03 2.4436951E-02 at 170iterations 7.2239275E-04 1.3880730E-02 at 180iterations finished qdiffx linear iterations at : 19:33:18 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 7.2239275E-04 1.3880730E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.73000 DelPhi exited at 19:33:19 15.728u 0.276s 0:16.40 97.5% 0+0k 0+0io 0pf+0w