Tue Oct 11 03:59:48 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 Tue Oct 11 2011 at 03:59:48 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6433192 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): -10.95900 37.01700 ymin,ymax (A): -25.60300 22.54800 zmin,zma (A): -10.13100 45.20700 x,y,z range (A): 47.97600 48.15100 55.33800 scale (grids/A): 0.6433192 object centre (A): 13.02900 -1.527499 17.53800 number of atom coordinates read : 2758 total number of charged atoms : 2605 net assigned charge : -0.8459793 assigned positive charge : 419.2458 centred at (gu) : 90.05170 90.29797 91.76727 assigned negative charge : -420.0923 centred at (gu) : 89.79848 90.18046 91.70663 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7428 nv = 96 ne = 84 npr = 57345 no. pairs analyzed = 57345 no. exposed pairs = 3310 no. arc points = 22859 no. surface atoms = 1105 nbur = 1653 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 4206 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3800000 number of dielectric boundary points 3589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2229 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9072 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8142252E-09 1.0023511E-08 midg,1,midg; midg,igrid,midg -1.6805719E-08 1.5428393E-08 1,midg,midg; igrid,midg,midg -3.6969812E-08 3.2778328E-08 gauss-seidel spectral radius is 0.9874870 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 03:59:49 rms-change max change #iterations 0.1591179 22.52303 at 10iterations 1.6260153E-02 2.515604 at 20iterations 1.7109857E-03 0.2495117 at 30iterations 1.9587952E-04 2.6151657E-02 at 40iterations 3.0840740E-05 4.4174194E-03 at 50iterations finished qdiffx linear iterations at : 03:59:52 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 3.0840740E-05 4.4174194E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 03:59:52 4.211u 0.258s 0:04.84 92.1% 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 Tue Oct 11 2011 at 03:59:52 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.929958 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): -10.95900 37.01700 ymin,ymax (A): -25.60300 22.54800 zmin,zma (A): -10.13100 45.20700 x,y,z range (A): 47.97600 48.15100 55.33800 scale (grids/A): 1.929958 object centre (A): 13.02900 -1.527499 17.53800 number of atom coordinates read : 2758 total number of charged atoms : 2605 net assigned charge : -0.8459793 assigned positive charge : 419.2458 centred at (gu) : 90.15440 90.89326 95.30135 assigned negative charge : -420.0923 centred at (gu) : 89.39503 90.54083 95.11977 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22859 grid for indexing accessible points = 1.400000 m= 29383 mr = 57374 m= 4541 mr = 21681 m= 272 mr = 2836 m= 9 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 790 time to turn everything in is 0.7300000 number of dielectric boundary points 32969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20530 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) : 0.6433192 object centre at (A) : 13.02900 -1.527499 17.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2414760E-02 -1.4399284E-02 midg,1,midg; midg,igrid,midg -1.3408909E-02 2.2677954E-02 1,midg,midg; igrid,midg,midg -2.0699952E-02 4.8518628E-02 gauss-seidel spectral radius is 0.9986792 estimated iterations to convergence 218 setup time was (sec) 1.050000 now iterating at: 03:59:54 rms-change max change #iterations 4.553603 203.6376 at 10iterations 2.168118 71.91847 at 20iterations 1.030752 33.26105 at 30iterations 0.4908662 15.41579 at 40iterations 0.2327645 8.095075 at 50iterations 0.1106751 3.376778 at 60iterations 5.2610043E-02 1.560036 at 70iterations 2.5021864E-02 0.7478848 at 80iterations 1.1892890E-02 0.3685827 at 90iterations 5.6441179E-03 0.1674881 at 100iterations 2.6924626E-03 9.2327118E-02 at 110iterations 1.2804030E-03 3.9101601E-02 at 120iterations finished qdiffx linear iterations at : 04:00:02 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 1.2804030E-03 3.9101601E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 04:00:03 9.836u 0.300s 0:10.50 96.4% 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 Tue Oct 11 2011 at 04:00:03 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.894937 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): -10.95900 37.01700 ymin,ymax (A): -25.60300 22.54800 zmin,zma (A): -10.13100 45.20700 x,y,z range (A): 47.97600 48.15100 55.33800 scale (grids/A): 2.894937 object centre (A): 13.02900 -1.527499 17.53800 number of atom coordinates read : 2758 total number of charged atoms : 2605 net assigned charge : -0.8459793 assigned positive charge : 419.2458 centred at (gu) : 90.23160 91.33997 97.95170 assigned negative charge : -420.0923 centred at (gu) : 89.09237 90.81126 97.67950 start vw surface at 0.1800000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 186932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22859 grid for indexing accessible points = 1.400000 m= 95548 mr = 138612 m= 33985 mr = 78586 m= 8168 mr = 27360 m= 1175 mr = 6208 m= 56 mr = 728 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 2614 time to turn everything in is 1.880000 number of dielectric boundary points 74351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 20835 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) : 1.929958 object centre at (A) : 13.02900 -1.527499 17.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8053145 8.9047827E-02 midg,1,midg; midg,igrid,midg -0.1509214 0.2978536 1,midg,midg; igrid,midg,midg -0.1277894 0.4273621 gauss-seidel spectral radius is 0.9992676 estimated iterations to convergence 292 setup time was (sec) 2.220000 now iterating at: 04:00:06 rms-change max change #iterations 10.56742 389.4856 at 10iterations 6.173334 130.0846 at 20iterations 3.593832 78.39906 at 30iterations 2.092134 50.93122 at 40iterations 1.213463 24.93313 at 50iterations 0.7032406 12.84581 at 60iterations 0.4070590 7.221526 at 70iterations 0.2358358 4.485696 at 80iterations 0.1363434 2.648876 at 90iterations 7.8766294E-02 1.398808 at 100iterations 4.5578327E-02 0.8422012 at 110iterations 2.6397936E-02 0.5671463 at 120iterations 1.5216561E-02 0.2511711 at 130iterations 8.8359592E-03 0.1647100 at 140iterations 5.0979303E-03 8.6978912E-02 at 150iterations 2.9660137E-03 5.7811737E-02 at 160iterations 1.7321045E-03 3.1112671E-02 at 170iterations 1.0153900E-03 1.9609690E-02 at 180iterations finished qdiffx linear iterations at : 04:00:20 total time elapsed so far: 16.75000 # loops : 180 mean,max change (kT/e) : 1.0153900E-03 1.9609690E-02 energy calculations done at 16.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.95000 DelPhi exited at 04:00:21 16.948u 0.348s 0:17.75 97.3% 0+0k 0+0io 0pf+0w