Sun Oct 9 13:56:24 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 Sun Oct 9 2011 at 13:56:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 0.7060130 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): -1.181000 45.50400 ymin,ymax (A): 36.28300 86.70700 zmin,zma (A): -24.66200 25.11000 x,y,z range (A): 46.68500 50.42400 49.77200 scale (grids/A): 0.7060130 object centre (A): 22.16150 61.49500 0.2240000 number of atom coordinates read : 2371 total number of charged atoms : 2230 net assigned charge : 3.500020 assigned positive charge : 361.0091 centred at (gu) : 90.09204 90.01673 91.63243 assigned negative charge : -357.5096 centred at (gu) : 90.23202 90.10656 91.55448 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8084 nv = 96 ne = 84 npr = 47773 no. pairs analyzed = 47773 no. exposed pairs = 3008 no. arc points = 21166 no. surface atoms = 997 nbur = 1374 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 4468 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2000000 number of dielectric boundary points 4053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1916 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8906 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0552150E-08 9.6922058E-08 midg,1,midg; midg,igrid,midg 7.6384964E-08 -2.1830239E-08 1,midg,midg; igrid,midg,midg 1.0161877E-07 -5.0814130E-08 gauss-seidel spectral radius is 0.9895757 estimated iterations to convergence 80 setup time was (sec) 0.4000000 now iterating at: 13:56:24 rms-change max change #iterations 0.2116747 24.57699 at 10iterations 2.6217375E-02 3.624207 at 20iterations 3.7897057E-03 0.5227509 at 30iterations 8.0720673E-04 0.1217613 at 40iterations 2.5001433E-04 3.7372589E-02 at 50iterations finished qdiffx linear iterations at : 13:56:27 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 2.5001433E-04 3.7372589E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 13:56:28 3.656u 0.213s 0:04.18 92.3% 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 Sun Oct 9 2011 at 13:56:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 2.118039 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): -1.181000 45.50400 ymin,ymax (A): 36.28300 86.70700 zmin,zma (A): -24.66200 25.11000 x,y,z range (A): 46.68500 50.42400 49.77200 scale (grids/A): 2.118039 object centre (A): 22.16150 61.49500 0.2240000 number of atom coordinates read : 2371 total number of charged atoms : 2230 net assigned charge : 3.500020 assigned positive charge : 361.0091 centred at (gu) : 90.27579 90.04976 94.89700 assigned negative charge : -357.5096 centred at (gu) : 90.69576 90.31940 94.66328 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21166 grid for indexing accessible points = 1.400000 m= 33341 mr = 59601 m= 6075 mr = 24947 m= 537 mr = 3839 m= 19 mr = 275 m= 0 mr = 8 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.4300000 number of dielectric boundary points 37029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17679 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) : 0.7060130 object centre at (A) : 22.16150 61.49500 0.2240000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3671938E-02 3.1930961E-02 midg,1,midg; midg,igrid,midg 0.1084199 4.3117544E-03 1,midg,midg; igrid,midg,midg 1.5618195E-03 -1.6978871E-02 gauss-seidel spectral radius is 0.9988657 estimated iterations to convergence 235 setup time was (sec) 0.6700000 now iterating at: 13:56:29 rms-change max change #iterations 4.985213 272.4581 at 10iterations 2.487871 85.56438 at 20iterations 1.241539 35.47994 at 30iterations 0.6242403 18.50835 at 40iterations 0.3126416 10.17565 at 50iterations 0.1570827 4.780994 at 60iterations 7.9126365E-02 2.313601 at 70iterations 3.9515816E-02 1.078025 at 80iterations 2.0009043E-02 0.5783463 at 90iterations 1.0205063E-02 0.3025150 at 100iterations 5.2463189E-03 0.1586761 at 110iterations 2.7780733E-03 8.1405640E-02 at 120iterations finished qdiffx linear iterations at : 13:56:36 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 2.7780733E-03 8.1405640E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 13:56:37 8.449u 0.223s 0:09.03 95.9% 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 Sun Oct 9 2011 at 13:56:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 3.177058 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): -1.181000 45.50400 ymin,ymax (A): 36.28300 86.70700 zmin,zma (A): -24.66200 25.11000 x,y,z range (A): 46.68500 50.42400 49.77200 scale (grids/A): 3.177058 object centre (A): 22.16150 61.49500 0.2240000 number of atom coordinates read : 2371 total number of charged atoms : 2230 net assigned charge : 3.500020 assigned positive charge : 361.0091 centred at (gu) : 90.41337 90.07446 97.34540 assigned negative charge : -357.5096 centred at (gu) : 91.04359 90.47906 96.99481 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 197545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21166 grid for indexing accessible points = 1.400000 m= 104775 mr = 143891 m= 41037 mr = 86350 m= 11176 mr = 33166 m= 2167 mr = 8490 m= 262 mr = 1561 m= 13 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 482 time to turn everything in is 1.340000 number of dielectric boundary points 83354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 17840 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) : 2.118039 object centre at (A) : 22.16150 61.49500 0.2240000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2517272 0.4741979 midg,1,midg; midg,igrid,midg 1.588080 -8.9364029E-02 1,midg,midg; igrid,midg,midg -2.9074073E-02 -0.1263407 gauss-seidel spectral radius is 0.9993114 estimated iterations to convergence 301 setup time was (sec) 1.600000 now iterating at: 13:56:39 rms-change max change #iterations 11.13866 450.2800 at 10iterations 6.623153 168.7405 at 20iterations 3.932612 86.45375 at 30iterations 2.337487 50.02027 at 40iterations 1.383757 27.11469 at 50iterations 0.8180636 15.04808 at 60iterations 0.4822265 8.956499 at 70iterations 0.2847044 5.184534 at 80iterations 0.1680439 3.007731 at 90iterations 9.9098049E-02 1.765617 at 100iterations 5.8514193E-02 0.9530163 at 110iterations 3.4738187E-02 0.6870933 at 120iterations 2.0753091E-02 0.3687954 at 130iterations 1.2593167E-02 0.2139511 at 140iterations 7.8741480E-03 0.1482677 at 150iterations 5.1195966E-03 0.1033554 at 160iterations 3.5353366E-03 7.4924469E-02 at 170iterations 2.6007122E-03 5.0979614E-02 at 180iterations finished qdiffx linear iterations at : 13:56:51 total time elapsed so far: 14.08000 # loops : 180 mean,max change (kT/e) : 2.6007122E-03 5.0979614E-02 energy calculations done at 14.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.21000 DelPhi exited at 13:56:52 14.216u 0.251s 0:14.74 98.1% 0+0k 0+0io 0pf+0w