Sat Oct 8 14:31:50 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 14:31:51 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 = 3047 !!! 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: 0.6149594 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): -13.92800 35.72300 ymin,ymax (A): -12.57900 45.31100 zmin,zma (A): -39.96400 12.52200 x,y,z range (A): 49.65100 57.89000 52.48600 scale (grids/A): 0.6149594 object centre (A): 10.89750 16.36600 -13.72100 number of atom coordinates read : 3047 total number of charged atoms : 2900 net assigned charge : 1.000006 assigned positive charge : 457.0156 centred at (gu) : 91.50208 91.82853 91.10640 assigned negative charge : -456.0163 centred at (gu) : 91.52583 91.76594 91.17712 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7435 nv = 96 ne = 84 npr = 64543 no. pairs analyzed = 64543 no. exposed pairs = 3526 no. arc points = 24120 no. surface atoms = 1202 nbur = 1845 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 4273 m= 2 mr = 30 m= 0 mr = 0 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 3484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2417 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2020671E-09 -5.2622511E-09 midg,1,midg; midg,igrid,midg -2.3338786E-09 7.3345507E-09 1,midg,midg; igrid,midg,midg 1.6302212E-09 -1.2935590E-09 gauss-seidel spectral radius is 0.9863368 estimated iterations to convergence 70 setup time was (sec) 0.6500000 now iterating at: 14:31:52 rms-change max change #iterations 0.1339694 18.87715 at 10iterations 1.2488585E-02 1.742413 at 20iterations 1.2485841E-03 0.1680412 at 30iterations 1.5260233E-04 2.2583008E-02 at 40iterations 2.5852905E-05 3.9863586E-03 at 50iterations finished qdiffx linear iterations at : 14:31:55 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 2.5852905E-05 3.9863586E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 14:31:56 4.558u 0.431s 0:05.25 94.8% 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 14:31:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3047 !!! 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: 1.844878 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): -13.92800 35.72300 ymin,ymax (A): -12.57900 45.31100 zmin,zma (A): -39.96400 12.52200 x,y,z range (A): 49.65100 57.89000 52.48600 scale (grids/A): 1.844878 object centre (A): 10.89750 16.36600 -13.72100 number of atom coordinates read : 3047 total number of charged atoms : 2900 net assigned charge : 1.000006 assigned positive charge : 457.0156 centred at (gu) : 94.50564 95.48518 93.31866 assigned negative charge : -456.0163 centred at (gu) : 94.57722 95.29751 93.53089 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24120 grid for indexing accessible points = 1.400000 m= 28514 mr = 59083 m= 3868 mr = 21172 m= 178 mr = 2259 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 32229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22726 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) : 0.6149594 object centre at (A) : 10.89750 16.36600 -13.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3831257E-02 7.3783952E-03 midg,1,midg; midg,igrid,midg -1.8757081E-02 4.2013451E-02 1,midg,midg; igrid,midg,midg 6.6995635E-03 -5.5766939E-03 gauss-seidel spectral radius is 0.9985792 estimated iterations to convergence 210 setup time was (sec) 0.9500000 now iterating at: 14:31:57 rms-change max change #iterations 4.353486 165.9995 at 10iterations 2.015438 63.72832 at 20iterations 0.9339364 29.72760 at 30iterations 0.4315359 13.13513 at 40iterations 0.1993276 6.349939 at 50iterations 9.2116378E-02 2.819748 at 60iterations 4.2625889E-02 1.346635 at 70iterations 1.9724708E-02 0.6014214 at 80iterations 9.1012558E-03 0.2733269 at 90iterations 4.2136349E-03 0.1355462 at 100iterations 1.9531016E-03 5.8524609E-02 at 110iterations 9.0371526E-04 2.6535034E-02 at 120iterations finished qdiffx linear iterations at : 14:32:07 total time elapsed so far: 10.73000 # loops : 120 mean,max change (kT/e) : 9.0371526E-04 2.6535034E-02 energy calculations done at 10.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.90000 DelPhi exited at 14:32:07 10.905u 0.475s 0:11.64 97.6% 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 14:32:07 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 = 3047 !!! 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: 2.767317 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): -13.92800 35.72300 ymin,ymax (A): -12.57900 45.31100 zmin,zma (A): -39.96400 12.52200 x,y,z range (A): 49.65100 57.89000 52.48600 scale (grids/A): 2.767317 object centre (A): 10.89750 16.36600 -13.72100 number of atom coordinates read : 3047 total number of charged atoms : 2900 net assigned charge : 1.000006 assigned positive charge : 457.0156 centred at (gu) : 96.75818 98.22739 94.97774 assigned negative charge : -456.0163 centred at (gu) : 96.86569 97.94611 95.29626 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 190884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24120 grid for indexing accessible points = 1.400000 m= 95544 mr = 143326 m= 31313 mr = 79093 m= 6624 mr = 24962 m= 701 mr = 4770 m= 19 mr = 378 m= 1 mr = 2 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 72556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 23197 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) : 1.844878 object centre at (A) : 10.89750 16.36600 -13.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1350795 0.2290847 midg,1,midg; midg,igrid,midg -0.1368556 0.6328578 1,midg,midg; igrid,midg,midg 0.1042266 -3.5148073E-02 gauss-seidel spectral radius is 0.9992466 estimated iterations to convergence 288 setup time was (sec) 2.110000 now iterating at: 14:32:10 rms-change max change #iterations 10.36366 372.9234 at 10iterations 6.045865 142.9428 at 20iterations 3.496154 72.73347 at 30iterations 2.013599 35.32818 at 40iterations 1.160103 22.69062 at 50iterations 0.6661034 12.62201 at 60iterations 0.3824180 6.831850 at 70iterations 0.2199704 3.879911 at 80iterations 0.1256636 2.270473 at 90iterations 7.2003953E-02 1.392208 at 100iterations 4.1268785E-02 0.7060509 at 110iterations 2.3609143E-02 0.4096680 at 120iterations 1.3550843E-02 0.2464905 at 130iterations 7.7618943E-03 0.1369572 at 140iterations 4.4439067E-03 8.4880829E-02 at 150iterations 2.5503647E-03 4.1407585E-02 at 160iterations 1.4615942E-03 2.5917053E-02 at 170iterations 8.4112375E-04 1.5335083E-02 at 180iterations finished qdiffx linear iterations at : 14:32:26 total time elapsed so far: 18.43000 # loops : 180 mean,max change (kT/e) : 8.4112375E-04 1.5335083E-02 energy calculations done at 18.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.60000 DelPhi exited at 14:32:27 18.604u 0.487s 0:19.36 98.5% 0+0k 0+0io 0pf+0w