Sat Oct 8 16:05:22 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 16:05:23 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6524448 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): -1.766000 45.75900 ymin,ymax (A): -16.10000 29.39700 zmin,zma (A): -17.65400 36.91000 x,y,z range (A): 47.52500 45.49700 54.56400 scale (grids/A): 0.6524448 object centre (A): 21.99650 6.648499 9.627999 number of atom coordinates read : 2336 total number of charged atoms : 2239 net assigned charge : 2.900002 assigned positive charge : 345.9181 centred at (gu) : 90.53829 88.64372 90.30780 assigned negative charge : -343.0188 centred at (gu) : 90.54973 88.77362 90.39156 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6668 nv = 96 ne = 84 npr = 48151 no. pairs analyzed = 48151 no. exposed pairs = 2824 no. arc points = 19533 no. surface atoms = 973 nbur = 1363 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3747 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3100000 number of dielectric boundary points 3217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1901 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7968 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6577316E-08 -6.8223747E-09 midg,1,midg; midg,igrid,midg 3.2264325E-08 -9.7702557E-09 1,midg,midg; igrid,midg,midg 6.6365393E-09 4.5892650E-09 gauss-seidel spectral radius is 0.9878011 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 16:05:23 rms-change max change #iterations 0.1484479 23.99220 at 10iterations 1.5715281E-02 2.184207 at 20iterations 1.6236380E-03 0.2043734 at 30iterations 1.7412637E-04 2.3525178E-02 at 40iterations 2.1543216E-05 3.4307241E-03 at 50iterations finished qdiffx linear iterations at : 16:05:28 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 2.1543216E-05 3.4307241E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.190000 DelPhi exited at 16:05:28 5.195u 0.406s 0:05.87 95.2% 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 16:05:28 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.957334 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): -1.766000 45.75900 ymin,ymax (A): -16.10000 29.39700 zmin,zma (A): -17.65400 36.91000 x,y,z range (A): 47.52500 45.49700 54.56400 scale (grids/A): 1.957334 object centre (A): 21.99650 6.648499 9.627999 number of atom coordinates read : 2336 total number of charged atoms : 2239 net assigned charge : 2.900002 assigned positive charge : 345.9181 centred at (gu) : 91.61433 85.93082 90.92305 assigned negative charge : -343.0188 centred at (gu) : 91.64897 86.32090 91.17464 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19533 grid for indexing accessible points = 1.400000 m= 26194 mr = 50627 m= 4564 mr = 19712 m= 307 mr = 3109 m= 3 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1011 time to turn everything in is 0.6000000 number of dielectric boundary points 29463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17651 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) : 0.6524448 object centre at (A) : 21.99650 6.648499 9.627999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7963333E-02 -1.8713605E-02 midg,1,midg; midg,igrid,midg 2.8436147E-02 -5.8079590E-03 1,midg,midg; igrid,midg,midg 1.3291480E-03 -3.5774566E-02 gauss-seidel spectral radius is 0.9986750 estimated iterations to convergence 218 setup time was (sec) 0.9100000 now iterating at: 16:05:30 rms-change max change #iterations 4.224053 169.2284 at 10iterations 1.991814 66.87865 at 20iterations 0.9456170 30.88020 at 30iterations 0.4481373 15.03878 at 40iterations 0.2111224 6.868786 at 50iterations 0.1005496 3.774928 at 60iterations 4.7526930E-02 1.389896 at 70iterations 2.2590932E-02 0.7587738 at 80iterations 1.0739145E-02 0.3873739 at 90iterations 5.0767977E-03 0.1628017 at 100iterations 2.4079338E-03 7.6894760E-02 at 110iterations 1.1508680E-03 3.6331177E-02 at 120iterations finished qdiffx linear iterations at : 16:05:40 total time elapsed so far: 11.48000 # loops : 120 mean,max change (kT/e) : 1.1508680E-03 3.6331177E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 16:05:41 11.654u 0.442s 0:12.36 97.8% 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 16:05:41 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2336 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.936002 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): -1.766000 45.75900 ymin,ymax (A): -16.10000 29.39700 zmin,zma (A): -17.65400 36.91000 x,y,z range (A): 47.52500 45.49700 54.56400 scale (grids/A): 2.936002 object centre (A): 21.99650 6.648499 9.627999 number of atom coordinates read : 2336 total number of charged atoms : 2239 net assigned charge : 2.900002 assigned positive charge : 345.9181 centred at (gu) : 92.42144 83.89619 91.38448 assigned negative charge : -343.0188 centred at (gu) : 92.47346 84.48136 91.76196 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 166406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19533 grid for indexing accessible points = 1.400000 m= 83682 mr = 122375 m= 31731 mr = 69092 m= 8726 mr = 26192 m= 1321 mr = 6941 m= 74 mr = 927 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.9599999 no. cavity mid-points inaccessible to solvent = 3371 time to turn everything in is 1.610000 number of dielectric boundary points 66382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 17910 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) : 1.957334 object centre at (A) : 21.99650 6.648499 9.627999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1731628 -0.2380764 midg,1,midg; midg,igrid,midg 0.2017423 -7.6961227E-02 1,midg,midg; igrid,midg,midg 2.3538103E-02 -0.5387013 gauss-seidel spectral radius is 0.9992627 estimated iterations to convergence 291 setup time was (sec) 1.980000 now iterating at: 16:05:43 rms-change max change #iterations 9.733498 509.9329 at 10iterations 5.674748 156.0624 at 20iterations 3.293661 73.94549 at 30iterations 1.915353 42.09796 at 40iterations 1.112231 22.39164 at 50iterations 0.6433293 11.31276 at 60iterations 0.3712581 7.144228 at 70iterations 0.2145377 4.062078 at 80iterations 0.1238952 3.188683 at 90iterations 7.1314797E-02 1.317016 at 100iterations 4.1062955E-02 0.7184944 at 110iterations 2.3690984E-02 0.4147625 at 120iterations 1.3632128E-02 0.2471511 at 130iterations 7.8545725E-03 0.1342678 at 140iterations 4.5189853E-03 8.1584930E-02 at 150iterations 2.6009372E-03 4.8610210E-02 at 160iterations 1.4963435E-03 2.7172804E-02 at 170iterations 8.6562993E-04 1.6582489E-02 at 180iterations finished qdiffx linear iterations at : 16:06:02 total time elapsed so far: 20.85000 # loops : 180 mean,max change (kT/e) : 8.6562993E-04 1.6582489E-02 energy calculations done at 20.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.04000 DelPhi exited at 16:06:03 21.049u 0.476s 0:21.82 98.5% 0+0k 0+0io 0pf+0w