Tue Oct 11 08:22:39 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 Tue Oct 11 2011 at 08:22:39 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: THR 174 has a net charge of -0.2720 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: 0.6065665 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): -12.25000 36.77900 ymin,ymax (A): 3.477000 51.83000 zmin,zma (A): -13.16400 45.52700 x,y,z range (A): 49.02900 48.35300 58.69100 scale (grids/A): 0.6065665 object centre (A): 12.26450 27.65350 16.18150 number of atom coordinates read : 2817 total number of charged atoms : 2663 net assigned charge : 4.228015 assigned positive charge : 426.4347 centred at (gu) : 90.39484 90.39445 92.31351 assigned negative charge : -422.2072 centred at (gu) : 90.15165 90.21991 92.33231 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6849 nv = 96 ne = 84 npr = 57031 no. pairs analyzed = 57031 no. exposed pairs = 3339 no. arc points = 23600 no. surface atoms = 1122 nbur = 1695 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3845 m= 0 mr = 33 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2302 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8670783E-09 2.0741284E-09 midg,1,midg; midg,igrid,midg -5.8464669E-09 1.1414093E-08 1,midg,midg; igrid,midg,midg -9.0201651E-09 1.4871449E-08 gauss-seidel spectral radius is 0.9859441 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 08:22:40 rms-change max change #iterations 0.1210535 17.73997 at 10iterations 1.0435982E-02 1.704638 at 20iterations 9.3316700E-04 0.1358585 at 30iterations 8.4806561E-05 1.0929108E-02 at 40iterations 1.0840668E-05 1.9397736E-03 at 50iterations finished qdiffx linear iterations at : 08:22:42 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0840668E-05 1.9397736E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:22:43 3.409u 0.148s 0:03.91 90.5% 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 08:22:43 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: THR 174 has a net charge of -0.2720 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: 1.819700 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): -12.25000 36.77900 ymin,ymax (A): 3.477000 51.83000 zmin,zma (A): -13.16400 45.52700 x,y,z range (A): 49.02900 48.35300 58.69100 scale (grids/A): 1.819700 object centre (A): 12.26450 27.65350 16.18150 number of atom coordinates read : 2817 total number of charged atoms : 2663 net assigned charge : 4.228015 assigned positive charge : 426.4347 centred at (gu) : 91.18427 91.18267 96.93983 assigned negative charge : -422.2072 centred at (gu) : 90.45453 90.65947 96.99687 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74640 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 26309 mr = 52813 m= 3544 mr = 19603 m= 172 mr = 2102 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 0.5700000 number of dielectric boundary points 30097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20800 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) : 0.6065665 object centre at (A) : 12.26450 27.65350 16.18150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5778228E-03 6.9301534E-03 midg,1,midg; midg,igrid,midg -1.3984798E-02 1.5535573E-02 1,midg,midg; igrid,midg,midg -8.4934337E-03 3.7053306E-02 gauss-seidel spectral radius is 0.9985271 estimated iterations to convergence 207 setup time was (sec) 0.8600000 now iterating at: 08:22:44 rms-change max change #iterations 4.078440 169.4109 at 10iterations 1.853448 67.62767 at 20iterations 0.8459916 32.29176 at 30iterations 0.3856819 12.74989 at 40iterations 0.1755712 6.810070 at 50iterations 8.0026127E-02 2.379150 at 60iterations 3.6559012E-02 1.093101 at 70iterations 1.6637767E-02 0.5716362 at 80iterations 7.5841825E-03 0.2419186 at 90iterations 3.4586298E-03 0.1133156 at 100iterations 1.5794674E-03 4.8831940E-02 at 110iterations 7.2141149E-04 2.3979187E-02 at 120iterations finished qdiffx linear iterations at : 08:22:50 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 7.2141149E-04 2.3979187E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:22:51 7.609u 0.184s 0:08.09 96.1% 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 08:22:51 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: THR 174 has a net charge of -0.2720 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: 2.729550 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): -12.25000 36.77900 ymin,ymax (A): 3.477000 51.83000 zmin,zma (A): -13.16400 45.52700 x,y,z range (A): 49.02900 48.35300 58.69100 scale (grids/A): 2.729550 object centre (A): 12.26450 27.65350 16.18150 number of atom coordinates read : 2817 total number of charged atoms : 2663 net assigned charge : 4.228015 assigned positive charge : 426.4347 centred at (gu) : 91.77616 91.77392 100.4094 assigned negative charge : -422.2072 centred at (gu) : 90.68175 90.98927 100.4952 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 173108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 87399 mr = 127983 m= 29571 mr = 72242 m= 6224 mr = 23889 m= 719 mr = 4563 m= 40 mr = 449 m= 0 mr = 16 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 3906 time to turn everything in is 1.380000 number of dielectric boundary points 67919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 21302 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) : 1.819700 object centre at (A) : 12.26450 27.65350 16.18150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1566438 0.2412302 midg,1,midg; midg,igrid,midg -0.1795532 0.1897589 1,midg,midg; igrid,midg,midg -8.1520095E-02 0.3319892 gauss-seidel spectral radius is 0.9992248 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 08:22:53 rms-change max change #iterations 9.713223 331.8444 at 10iterations 5.610655 158.2702 at 20iterations 3.227712 68.72374 at 30iterations 1.853960 52.39385 at 40iterations 1.061853 23.34043 at 50iterations 0.6062806 11.65001 at 60iterations 0.3452572 7.657236 at 70iterations 0.1968790 3.706257 at 80iterations 0.1121404 2.062948 at 90iterations 6.3790642E-02 1.232552 at 100iterations 3.6262982E-02 0.7061872 at 110iterations 2.0617360E-02 0.3745842 at 120iterations 1.1725990E-02 0.2293644 at 130iterations 6.6640540E-03 0.1389275 at 140iterations 3.8040101E-03 7.8883648E-02 at 150iterations 2.1714072E-03 4.5055389E-02 at 160iterations 1.2445343E-03 2.6584625E-02 at 170iterations 7.2181382E-04 1.6640663E-02 at 180iterations finished qdiffx linear iterations at : 08:23:04 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 7.2181382E-04 1.6640663E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 08:23:04 12.530u 0.220s 0:13.09 97.4% 0+0k 0+0io 0pf+0w