Tue Oct 11 04:24:57 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+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 04:24:58 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 79 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6349093 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): -11.37000 36.82700 ymin,ymax (A): -26.79500 21.65500 zmin,zma (A): -10.36000 45.71100 x,y,z range (A): 48.19700 48.45000 56.07100 scale (grids/A): 0.6349093 object centre (A): 12.72850 -2.570001 17.67550 number of atom coordinates read : 2693 total number of charged atoms : 2545 net assigned charge : 1.514015 assigned positive charge : 410.5659 centred at (gu) : 90.15923 90.21933 91.99618 assigned negative charge : -409.0523 centred at (gu) : 89.88691 90.05547 91.95341 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 55190 no. pairs analyzed = 55190 no. exposed pairs = 3208 no. arc points = 22426 no. surface atoms = 1078 nbur = 1615 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 4188 m= 0 mr = 42 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2000000 number of dielectric boundary points 3433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2305 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7971221E-09 9.7391233E-09 midg,1,midg; midg,igrid,midg -1.5250908E-08 1.9825546E-08 1,midg,midg; igrid,midg,midg -2.7153934E-08 3.0966344E-08 gauss-seidel spectral radius is 0.9871534 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 04:24:58 rms-change max change #iterations 0.1473253 20.35708 at 10iterations 1.4592223E-02 2.249268 at 20iterations 1.5120417E-03 0.2048969 at 30iterations 2.0066711E-04 3.3729553E-02 at 40iterations 4.1521082E-05 6.1702728E-03 at 50iterations finished qdiffx linear iterations at : 04:25:01 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.1521082E-05 6.1702728E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 04:25:01 3.389u 0.165s 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 04:25:02 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 79 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.904728 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): -11.37000 36.82700 ymin,ymax (A): -26.79500 21.65500 zmin,zma (A): -10.36000 45.71100 x,y,z range (A): 48.19700 48.45000 56.07100 scale (grids/A): 1.904728 object centre (A): 12.72850 -2.570001 17.67550 number of atom coordinates read : 2693 total number of charged atoms : 2545 net assigned charge : 1.514015 assigned positive charge : 410.5659 centred at (gu) : 90.47727 90.65754 95.98794 assigned negative charge : -409.0523 centred at (gu) : 89.66066 90.16609 95.85989 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22426 grid for indexing accessible points = 1.400000 m= 29624 mr = 55849 m= 4752 mr = 22510 m= 305 mr = 3131 m= 2 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 229 time to turn everything in is 0.3800000 number of dielectric boundary points 31615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20011 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) : 0.6349093 object centre at (A) : 12.72850 -2.570001 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2415472E-02 -8.0015976E-03 midg,1,midg; midg,igrid,midg -1.4024704E-02 2.2072401E-02 1,midg,midg; igrid,midg,midg -1.1062939E-02 5.9335995E-02 gauss-seidel spectral radius is 0.9986430 estimated iterations to convergence 215 setup time was (sec) 0.5900000 now iterating at: 04:25:02 rms-change max change #iterations 4.421519 178.5646 at 10iterations 2.084411 71.24310 at 20iterations 0.9810660 27.58774 at 30iterations 0.4622871 14.58543 at 40iterations 0.2163416 6.872814 at 50iterations 0.1022660 2.964157 at 60iterations 4.8023362E-02 1.616590 at 70iterations 2.2646628E-02 0.6973302 at 80iterations 1.0631191E-02 0.3377838 at 90iterations 5.0181304E-03 0.1839418 at 100iterations 2.3723738E-03 6.8344116E-02 at 110iterations 1.1227583E-03 3.5240173E-02 at 120iterations finished qdiffx linear iterations at : 04:25:09 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.1227583E-03 3.5240173E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 04:25:10 7.795u 0.207s 0:08.31 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 04:25:10 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 79 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.857092 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): -11.37000 36.82700 ymin,ymax (A): -26.79500 21.65500 zmin,zma (A): -10.36000 45.71100 x,y,z range (A): 48.19700 48.45000 56.07100 scale (grids/A): 2.857092 object centre (A): 12.72850 -2.570001 17.67550 number of atom coordinates read : 2693 total number of charged atoms : 2545 net assigned charge : 1.514015 assigned positive charge : 410.5659 centred at (gu) : 90.71588 90.98626 98.98183 assigned negative charge : -409.0523 centred at (gu) : 89.49088 90.24924 98.78966 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 181366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22426 grid for indexing accessible points = 1.400000 m= 95303 mr = 134727 m= 35575 mr = 79479 m= 8611 mr = 29050 m= 1342 mr = 6729 m= 91 mr = 983 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 822 time to turn everything in is 0.9900000 number of dielectric boundary points 71270 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 20358 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) : 1.904728 object centre at (A) : 12.72850 -2.570001 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5706729 0.1524443 midg,1,midg; midg,igrid,midg -0.1701796 0.2681225 1,midg,midg; igrid,midg,midg -8.1031330E-02 0.5436281 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.220000 now iterating at: 04:25:11 rms-change max change #iterations 10.30705 497.6558 at 10iterations 6.038189 139.5760 at 20iterations 3.515811 86.95000 at 30iterations 2.044844 44.44924 at 40iterations 1.185442 21.29435 at 50iterations 0.6850684 13.81153 at 60iterations 0.3949824 7.264256 at 70iterations 0.2278520 4.166967 at 80iterations 0.1314454 2.336063 at 90iterations 7.6001428E-02 1.390787 at 100iterations 4.3789733E-02 0.8133926 at 110iterations 2.5164092E-02 0.4276375 at 120iterations 1.4521512E-02 0.2752824 at 130iterations 8.4092841E-03 0.1462379 at 140iterations 4.8608356E-03 8.4944010E-02 at 150iterations 2.8345629E-03 5.2350044E-02 at 160iterations 1.6616323E-03 2.7885437E-02 at 170iterations 9.9339162E-04 1.9252777E-02 at 180iterations finished qdiffx linear iterations at : 04:25:23 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 9.9339162E-04 1.9252777E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 04:25:23 12.652u 0.217s 0:13.15 97.7% 0+0k 0+0io 0pf+0w