Mon Oct 10 09:45:24 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 Mon Oct 10 2011 at 09:45:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5729829 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): 113.2480 175.3790 ymin,ymax (A): -43.69800 10.17100 zmin,zma (A): 45.89500 101.6520 x,y,z range (A): 62.13100 53.86900 55.75700 scale (grids/A): 0.5729829 object centre (A): 144.3135 -16.76350 73.77350 number of atom coordinates read : 2923 total number of charged atoms : 2770 net assigned charge : 8.014016 assigned positive charge : 428.8518 centred at (gu) : 89.40311 89.40125 89.79243 assigned negative charge : -420.8383 centred at (gu) : 89.43452 89.45763 89.63139 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6422 nv = 96 ne = 84 npr = 56500 no. pairs analyzed = 56500 no. exposed pairs = 4577 no. arc points = 33636 no. surface atoms = 1499 nbur = 1424 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 321 mr = 2677 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3303 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4101658E-09 3.7780166E-09 midg,1,midg; midg,igrid,midg 2.6347373E-09 3.8235340E-10 1,midg,midg; igrid,midg,midg 2.1635540E-09 7.4246642E-10 gauss-seidel spectral radius is 0.9842988 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 09:45:25 rms-change max change #iterations 9.0606086E-02 15.80336 at 10iterations 6.6846511E-03 1.055651 at 20iterations 5.0003838E-04 7.7590942E-02 at 30iterations 4.2955653E-05 6.1454773E-03 at 40iterations 5.9580930E-06 7.6675415E-04 at 50iterations finished qdiffx linear iterations at : 09:45:27 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 5.9580930E-06 7.6675415E-04 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 09:45:28 3.363u 0.142s 0:04.16 84.1% 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 Mon Oct 10 2011 at 09:45:28 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.718949 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): 113.2480 175.3790 ymin,ymax (A): -43.69800 10.17100 zmin,zma (A): 45.89500 101.6520 x,y,z range (A): 62.13100 53.86900 55.75700 scale (grids/A): 1.718949 object centre (A): 144.3135 -16.76350 73.77350 number of atom coordinates read : 2923 total number of charged atoms : 2770 net assigned charge : 8.014016 assigned positive charge : 428.8518 centred at (gu) : 88.20864 88.20330 89.37650 assigned negative charge : -420.8383 centred at (gu) : 88.30316 88.37263 88.89397 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33636 grid for indexing accessible points = 1.400000 m= 21293 mr = 40144 m= 2684 mr = 13296 m= 114 mr = 1153 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.5300000 number of dielectric boundary points 37784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21454 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) : 0.5729829 object centre at (A) : 144.3135 -16.76350 73.77350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9781028E-03 3.0213218E-02 midg,1,midg; midg,igrid,midg 1.2760812E-02 1.0074398E-02 1,midg,midg; igrid,midg,midg 2.3609858E-03 4.5690411E-03 gauss-seidel spectral radius is 0.9983972 estimated iterations to convergence 198 setup time was (sec) 0.8200000 now iterating at: 09:45:29 rms-change max change #iterations 3.623220 176.4701 at 10iterations 1.583950 65.54222 at 20iterations 0.6940973 30.61917 at 30iterations 0.3038938 11.52299 at 40iterations 0.1328024 5.785828 at 50iterations 5.8372647E-02 2.178047 at 60iterations 2.5518660E-02 0.9854851 at 70iterations 1.1138181E-02 0.3705139 at 80iterations 4.9081859E-03 0.1931076 at 90iterations 2.1595701E-03 7.7167511E-02 at 100iterations 9.4454491E-04 3.4234524E-02 at 110iterations 4.1509760E-04 1.5071243E-02 at 120iterations finished qdiffx linear iterations at : 09:45:36 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 4.1509760E-04 1.5071243E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 09:45:37 7.716u 0.156s 0:08.34 94.2% 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 Mon Oct 10 2011 at 09:45:37 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.578423 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): 113.2480 175.3790 ymin,ymax (A): -43.69800 10.17100 zmin,zma (A): 45.89500 101.6520 x,y,z range (A): 62.13100 53.86900 55.75700 scale (grids/A): 2.578423 object centre (A): 144.3135 -16.76350 73.77350 number of atom coordinates read : 2923 total number of charged atoms : 2770 net assigned charge : 8.014016 assigned positive charge : 428.8518 centred at (gu) : 87.31276 87.30471 89.06474 assigned negative charge : -420.8383 centred at (gu) : 87.45458 87.55876 88.34091 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 157384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33636 grid for indexing accessible points = 1.400000 m= 69816 mr = 99497 m= 22947 mr = 51101 m= 4188 mr = 16293 m= 343 mr = 2363 m= 10 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 1.280000 number of dielectric boundary points 85289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 22156 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) : 1.718949 object centre at (A) : 144.3135 -16.76350 73.77350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4186874E-02 0.4174532 midg,1,midg; midg,igrid,midg 0.1677988 0.1548159 1,midg,midg; igrid,midg,midg 7.1054764E-02 -6.3922526E-03 gauss-seidel spectral radius is 0.9992292 estimated iterations to convergence 284 setup time was (sec) 1.570000 now iterating at: 09:45:39 rms-change max change #iterations 9.330868 358.9609 at 10iterations 5.545841 151.4249 at 20iterations 3.247238 81.54187 at 30iterations 1.883460 43.93441 at 40iterations 1.087808 24.27616 at 50iterations 0.6260945 14.19110 at 60iterations 0.3593043 8.085808 at 70iterations 0.2060895 4.726706 at 80iterations 0.1176608 2.966572 at 90iterations 6.7138806E-02 1.381075 at 100iterations 3.8369466E-02 0.8498888 at 110iterations 2.1785153E-02 0.4860058 at 120iterations 1.2392660E-02 0.2681999 at 130iterations 7.0473640E-03 0.1531296 at 140iterations 4.0007420E-03 7.8971863E-02 at 150iterations 2.2788253E-03 4.5137405E-02 at 160iterations 1.2913833E-03 2.8685927E-02 at 170iterations 7.3538290E-04 1.4889717E-02 at 180iterations finished qdiffx linear iterations at : 09:45:49 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 7.3538290E-04 1.4889717E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 09:45:50 12.132u 0.198s 0:12.94 95.2% 0+0k 0+0io 0pf+0w