Mon Oct 10 16:12:52 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 16:12:52 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3845 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5557811 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): 7.494000 56.61300 ymin,ymax (A): 52.91500 116.9690 zmin,zma (A): -35.65800 26.11800 x,y,z range (A): 49.11900 64.05400 61.77600 scale (grids/A): 0.5557811 object centre (A): 32.05350 84.94200 -4.770000 number of atom coordinates read : 3845 total number of charged atoms : 3755 net assigned charge : 6.500011 assigned positive charge : 573.9083 centred at (gu) : 89.63583 90.41144 91.86903 assigned negative charge : -567.4111 centred at (gu) : 89.59305 90.49575 91.85680 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7961 nv = 96 ne = 84 npr = 76040 no. pairs analyzed = 76040 no. exposed pairs = 4915 no. arc points = 34242 no. surface atoms = 1643 nbur = 2202 mkacc time = 0.2300000 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= 348 mr = 4297 m= 0 mr = 12 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3512 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8866681E-10 1.1605540E-09 midg,1,midg; midg,igrid,midg 1.4495319E-09 -4.9028687E-10 1,midg,midg; igrid,midg,midg 7.5017478E-11 1.0138465E-09 gauss-seidel spectral radius is 0.9833758 estimated iterations to convergence 64 setup time was (sec) 0.8000000 now iterating at: 16:12:53 rms-change max change #iterations 9.2255361E-02 13.53471 at 10iterations 6.5991734E-03 1.059532 at 20iterations 6.7833666E-04 0.1138611 at 30iterations 1.7968089E-04 2.8818130E-02 at 40iterations 6.6556764E-05 9.1934204E-03 at 50iterations finished qdiffx linear iterations at : 16:12:56 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 6.6556764E-05 9.1934204E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 16:12:57 4.406u 0.204s 0:04.88 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 16:12:57 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3845 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.667343 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): 7.494000 56.61300 ymin,ymax (A): 52.91500 116.9690 zmin,zma (A): -35.65800 26.11800 x,y,z range (A): 49.11900 64.05400 61.77600 scale (grids/A): 1.667343 object centre (A): 32.05350 84.94200 -4.770000 number of atom coordinates read : 3845 total number of charged atoms : 3755 net assigned charge : 6.500011 assigned positive charge : 573.9083 centred at (gu) : 88.90656 91.23315 95.60588 assigned negative charge : -567.4111 centred at (gu) : 88.77889 91.48682 95.57016 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 88690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34242 grid for indexing accessible points = 1.400000 m= 29217 mr = 61880 m= 3460 mr = 20475 m= 103 mr = 1861 m= 0 mr = 15 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 546 time to turn everything in is 0.7900000 number of dielectric boundary points 37239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 28969 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) : 0.5557811 object centre at (A) : 32.05350 84.94200 -4.770000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8403092E-03 3.8400061E-02 midg,1,midg; midg,igrid,midg 1.8789450E-02 1.4874099E-02 1,midg,midg; igrid,midg,midg 9.1652659E-04 -6.2241163E-03 gauss-seidel spectral radius is 0.9983609 estimated iterations to convergence 196 setup time was (sec) 1.160000 now iterating at: 16:12:58 rms-change max change #iterations 3.995425 158.9648 at 10iterations 1.749886 56.45879 at 20iterations 0.7607001 24.29390 at 30iterations 0.3317831 10.57446 at 40iterations 0.1452126 4.997200 at 50iterations 6.3472740E-02 2.093222 at 60iterations 2.7662696E-02 0.8694077 at 70iterations 1.2143607E-02 0.4599333 at 80iterations 5.3199339E-03 0.1614990 at 90iterations 2.3663333E-03 7.7026367E-02 at 100iterations 1.0790476E-03 3.4659386E-02 at 110iterations 5.1805872E-04 1.6269684E-02 at 120iterations finished qdiffx linear iterations at : 16:13:06 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 5.1805872E-04 1.6269684E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 16:13:07 9.703u 0.219s 0:10.19 97.2% 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 16:13:07 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3845 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.501015 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): 7.494000 56.61300 ymin,ymax (A): 52.91500 116.9690 zmin,zma (A): -35.65800 26.11800 x,y,z range (A): 49.11900 64.05400 61.77600 scale (grids/A): 2.501015 object centre (A): 32.05350 84.94200 -4.770000 number of atom coordinates read : 3845 total number of charged atoms : 3755 net assigned charge : 6.500011 assigned positive charge : 573.9083 centred at (gu) : 88.35947 91.84949 98.40833 assigned negative charge : -567.4111 centred at (gu) : 88.16801 92.23020 98.35506 start vw surface at 0.2300000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 206124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34242 grid for indexing accessible points = 1.400000 m= 99778 mr = 151606 m= 30705 mr = 79523 m= 5712 mr = 23506 m= 469 mr = 4001 m= 9 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1792 time to turn everything in is 1.970000 number of dielectric boundary points 83930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 30018 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) : 1.667343 object centre at (A) : 32.05350 84.94200 -4.770000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1202558 0.9198658 midg,1,midg; midg,igrid,midg 0.2415058 0.3523516 1,midg,midg; igrid,midg,midg 1.8800629E-02 -0.1158255 gauss-seidel spectral radius is 0.9992196 estimated iterations to convergence 283 setup time was (sec) 2.360000 now iterating at: 16:13:09 rms-change max change #iterations 10.24020 342.3180 at 10iterations 5.977733 156.9795 at 20iterations 3.484281 80.12424 at 30iterations 2.014219 42.78858 at 40iterations 1.163170 24.30254 at 50iterations 0.6690930 12.67524 at 60iterations 0.3842378 7.592148 at 70iterations 0.2196440 4.019866 at 80iterations 0.1255218 2.297079 at 90iterations 7.1723089E-02 1.349365 at 100iterations 4.0854983E-02 0.8148817 at 110iterations 2.3326840E-02 0.4708977 at 120iterations 1.3293409E-02 0.2390099 at 130iterations 7.5778291E-03 0.1348934 at 140iterations 4.3259989E-03 7.8536987E-02 at 150iterations 2.4832573E-03 4.2304993E-02 at 160iterations 1.4358017E-03 2.6438713E-02 at 170iterations 8.4727403E-04 1.5213013E-02 at 180iterations finished qdiffx linear iterations at : 16:13:23 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 8.4727403E-04 1.5213013E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.92000 DelPhi exited at 16:13:23 15.925u 0.251s 0:16.66 97.0% 0+0k 0+0io 0pf+0w