Mon Oct 10 14:01:57 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 Mon Oct 10 2011 at 14:01:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 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: 0.6084118 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): -9.403000 43.14700 ymin,ymax (A): 25.36100 80.40200 zmin,zma (A): 100.3960 158.9090 x,y,z range (A): 52.55000 55.04100 58.51300 scale (grids/A): 0.6084118 object centre (A): 16.87200 52.88150 129.6525 number of atom coordinates read : 2947 total number of charged atoms : 2839 net assigned charge : 1.000019 assigned positive charge : 437.0119 centred at (gu) : 89.40256 89.21767 90.31184 assigned negative charge : -436.0135 centred at (gu) : 89.40094 89.08975 90.23241 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 56942 no. pairs analyzed = 56942 no. exposed pairs = 4190 no. arc points = 29181 no. surface atoms = 1377 nbur = 1570 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 418 mr = 3798 m= 0 mr = 40 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2906 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9313 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3822640E-09 5.1331539E-09 midg,1,midg; midg,igrid,midg -7.5038109E-09 6.1075398E-09 1,midg,midg; igrid,midg,midg 5.9919791E-10 6.1257321E-10 gauss-seidel spectral radius is 0.9860634 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 14:01:58 rms-change max change #iterations 0.1202638 20.21716 at 10iterations 1.0468641E-02 1.662907 at 20iterations 9.6337614E-04 0.1370239 at 30iterations 1.3636945E-04 2.2398233E-02 at 40iterations 3.7716367E-05 6.4325333E-03 at 50iterations finished qdiffx linear iterations at : 14:02:00 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.7716367E-05 6.4325333E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:02:01 3.338u 0.181s 0:04.59 76.4% 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 Mon Oct 10 2011 at 14:02:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.825235 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): -9.403000 43.14700 ymin,ymax (A): 25.36100 80.40200 zmin,zma (A): 100.3960 158.9090 x,y,z range (A): 52.55000 55.04100 58.51300 scale (grids/A): 1.825235 object centre (A): 16.87200 52.88150 129.6525 number of atom coordinates read : 2947 total number of charged atoms : 2839 net assigned charge : 1.000019 assigned positive charge : 437.0119 centred at (gu) : 88.20678 87.65224 90.93459 assigned negative charge : -436.0135 centred at (gu) : 88.20275 87.26901 90.69673 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29181 grid for indexing accessible points = 1.400000 m= 28680 mr = 53462 m= 4601 mr = 20033 m= 264 mr = 2596 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 38695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22233 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) : 0.6084118 object centre at (A) : 16.87200 52.88150 129.6525 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8583053E-02 -6.7274035E-03 midg,1,midg; midg,igrid,midg -9.5204432E-03 5.0469898E-03 1,midg,midg; igrid,midg,midg 7.9598714E-04 5.0717872E-03 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.9100000 now iterating at: 14:02:03 rms-change max change #iterations 4.186211 207.9402 at 10iterations 1.921723 78.42555 at 20iterations 0.8808646 29.69407 at 30iterations 0.4075057 12.60509 at 40iterations 0.1881284 5.851429 at 50iterations 8.6738504E-02 2.845615 at 60iterations 4.0120315E-02 1.245315 at 70iterations 1.8424388E-02 0.5958347 at 80iterations 8.5441666E-03 0.3208489 at 90iterations 3.9313375E-03 0.1645489 at 100iterations 1.8198700E-03 5.3373337E-02 at 110iterations 8.4633823E-04 2.7262688E-02 at 120iterations finished qdiffx linear iterations at : 14:02:09 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 8.4633823E-04 2.7262688E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:02:11 7.779u 0.264s 0:09.18 87.4% 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 Mon Oct 10 2011 at 14:02:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.737853 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): -9.403000 43.14700 ymin,ymax (A): 25.36100 80.40200 zmin,zma (A): 100.3960 158.9090 x,y,z range (A): 52.55000 55.04100 58.51300 scale (grids/A): 2.737853 object centre (A): 16.87200 52.88150 129.6525 number of atom coordinates read : 2947 total number of charged atoms : 2839 net assigned charge : 1.000019 assigned positive charge : 437.0119 centred at (gu) : 87.30984 86.47809 91.40162 assigned negative charge : -436.0135 centred at (gu) : 87.30399 85.90350 91.04517 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 188162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29181 grid for indexing accessible points = 1.400000 m= 91900 mr = 131247 m= 33367 mr = 72061 m= 8168 mr = 25598 m= 1073 mr = 5779 m= 56 mr = 604 m= 1 mr = 18 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 87421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 22706 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) : 1.825235 object centre at (A) : 16.87200 52.88150 129.6525 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4532217 -0.2931944 midg,1,midg; midg,igrid,midg 5.3962357E-03 0.1064617 1,midg,midg; igrid,midg,midg 5.7255886E-02 7.6827109E-02 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.810000 now iterating at: 14:02:13 rms-change max change #iterations 10.27630 329.1242 at 10iterations 6.151274 168.7787 at 20iterations 3.636322 91.07460 at 30iterations 2.137245 46.40124 at 40iterations 1.249981 25.85653 at 50iterations 0.7285356 15.19698 at 60iterations 0.4239848 8.501624 at 70iterations 0.2458005 4.601665 at 80iterations 0.1424921 2.685562 at 90iterations 8.2487509E-02 1.426631 at 100iterations 4.7691468E-02 0.8808594 at 110iterations 2.7536405E-02 0.5255508 at 120iterations 1.5939983E-02 0.2856884 at 130iterations 9.1853179E-03 0.1694031 at 140iterations 5.2957530E-03 9.5676422E-02 at 150iterations 3.0671707E-03 5.1385880E-02 at 160iterations 1.7658004E-03 3.1616211E-02 at 170iterations 1.0217574E-03 1.8848419E-02 at 180iterations finished qdiffx linear iterations at : 14:02:24 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 1.0217574E-03 1.8848419E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:02:25 12.787u 0.288s 0:13.87 94.1% 0+0k 0+0io 0pf+0w