Mon Oct 10 14:15:03 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 14:15:03 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 !!! WARNING: ADP 670 has a net charge of -2.0000 !!! WARNING: MG6 672 has a net charge of 1.4000 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: 0.5814524 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): -8.816999 52.40900 ymin,ymax (A): -15.91700 34.41000 zmin,zma (A): 79.22800 130.7160 x,y,z range (A): 61.22600 50.32700 51.48800 scale (grids/A): 0.5814524 object centre (A): 21.79600 9.246500 104.9720 number of atom coordinates read : 2639 total number of charged atoms : 2497 net assigned charge : -4.599992 assigned positive charge : 410.1266 centred at (gu) : 92.18301 89.95976 89.32972 assigned negative charge : -414.7274 centred at (gu) : 92.15852 90.03364 89.39614 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5993 nv = 96 ne = 84 npr = 51226 no. pairs analyzed = 51226 no. exposed pairs = 3703 no. arc points = 25783 no. surface atoms = 1246 nbur = 1393 mkacc time = 9.0000004E-02 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= 286 mr = 2918 m= 0 mr = 26 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0630127E-10 -2.1473221E-09 midg,1,midg; midg,igrid,midg 5.0024251E-10 -2.6461331E-09 1,midg,midg; igrid,midg,midg -9.7468378E-10 -8.8636043E-10 gauss-seidel spectral radius is 0.9847118 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 14:15:04 rms-change max change #iterations 9.9468149E-02 17.51477 at 10iterations 7.7050454E-03 1.303360 at 20iterations 6.1034557E-04 0.1019001 at 30iterations 4.7571069E-05 7.3051453E-03 at 40iterations 4.0739355E-06 6.8092346E-04 at 50iterations finished qdiffx linear iterations at : 14:15:07 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 4.0739355E-06 6.8092346E-04 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 14:15:08 3.703u 0.217s 0:04.62 84.6% 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 14:15:08 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 !!! WARNING: ADP 670 has a net charge of -2.0000 !!! WARNING: MG6 672 has a net charge of 1.4000 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: 1.744357 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): -8.816999 52.40900 ymin,ymax (A): -15.91700 34.41000 zmin,zma (A): 79.22800 130.7160 x,y,z range (A): 61.22600 50.32700 51.48800 scale (grids/A): 1.744357 object centre (A): 21.79600 9.246500 104.9720 number of atom coordinates read : 2639 total number of charged atoms : 2497 net assigned charge : -4.599992 assigned positive charge : 410.1266 centred at (gu) : 96.54836 89.87864 87.98846 assigned negative charge : -414.7274 centred at (gu) : 96.47525 90.10079 88.18791 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25783 grid for indexing accessible points = 1.400000 m= 21561 mr = 42416 m= 2869 mr = 14522 m= 139 mr = 1478 m= 0 mr = 23 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 30966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19353 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) : 0.5814524 object centre at (A) : 21.79600 9.246500 104.9720 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1354962E-02 -2.4642417E-02 midg,1,midg; midg,igrid,midg -3.6497947E-03 -1.4391740E-02 1,midg,midg; igrid,midg,midg 2.0834418E-02 1.8423047E-02 gauss-seidel spectral radius is 0.9983964 estimated iterations to convergence 198 setup time was (sec) 0.5600000 now iterating at: 14:15:08 rms-change max change #iterations 3.754071 197.4112 at 10iterations 1.633535 66.31306 at 20iterations 0.7189178 27.81175 at 30iterations 0.3146383 12.24392 at 40iterations 0.1384360 4.986496 at 50iterations 6.0837708E-02 2.120147 at 60iterations 2.6698254E-02 0.9650269 at 70iterations 1.1691852E-02 0.4588776 at 80iterations 5.1449863E-03 0.2061768 at 90iterations 2.2615306E-03 8.6780548E-02 at 100iterations 9.9286728E-04 3.6863327E-02 at 110iterations 4.3577261E-04 1.5737534E-02 at 120iterations finished qdiffx linear iterations at : 14:15:16 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 4.3577261E-04 1.5737534E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 14:15:16 8.028u 0.232s 0:08.67 95.1% 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 14:15:16 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 !!! WARNING: ADP 670 has a net charge of -2.0000 !!! WARNING: MG6 672 has a net charge of 1.4000 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: 2.616536 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): -8.816999 52.40900 ymin,ymax (A): -15.91700 34.41000 zmin,zma (A): 79.22800 130.7160 x,y,z range (A): 61.22600 50.32700 51.48800 scale (grids/A): 2.616536 object centre (A): 21.79600 9.246500 104.9720 number of atom coordinates read : 2639 total number of charged atoms : 2497 net assigned charge : -4.599992 assigned positive charge : 410.1266 centred at (gu) : 99.82229 89.81773 86.98241 assigned negative charge : -414.7274 centred at (gu) : 99.71287 90.15123 87.28192 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25783 grid for indexing accessible points = 1.400000 m= 71212 mr = 104290 m= 23131 mr = 55236 m= 4729 mr = 17052 m= 526 mr = 3116 m= 26 mr = 322 m= 0 mr = 3 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 69846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 19967 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) : 1.744357 object centre at (A) : 21.79600 9.246500 104.9720 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1461227 -0.3188234 midg,1,midg; midg,igrid,midg -7.4954405E-02 -0.1281913 1,midg,midg; igrid,midg,midg 0.3402131 0.1717139 gauss-seidel spectral radius is 0.9992023 estimated iterations to convergence 280 setup time was (sec) 1.070000 now iterating at: 14:15:18 rms-change max change #iterations 9.464469 336.1516 at 10iterations 5.533244 152.3389 at 20iterations 3.190042 79.39622 at 30iterations 1.826811 39.42073 at 40iterations 1.044736 21.94274 at 50iterations 0.5935664 13.13956 at 60iterations 0.3365844 7.529260 at 70iterations 0.1906857 3.815332 at 80iterations 0.1078127 2.220093 at 90iterations 6.0794666E-02 1.205793 at 100iterations 3.4367211E-02 0.6946716 at 110iterations 1.9334866E-02 0.4226379 at 120iterations 1.0910654E-02 0.2158728 at 130iterations 6.1579486E-03 0.1391811 at 140iterations 3.4685859E-03 6.8454742E-02 at 150iterations 1.9610927E-03 4.8213959E-02 at 160iterations 1.1126841E-03 2.2230625E-02 at 170iterations 6.3472288E-04 1.3401031E-02 at 180iterations finished qdiffx linear iterations at : 14:15:30 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 6.3472288E-04 1.3401031E-02 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 14:15:30 13.306u 0.251s 0:13.91 97.4% 0+0k 0+0io 0pf+0w