Mon Oct 10 17:16:48 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 Mon Oct 10 2011 at 17:16:48 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 = 2752 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: 0.5422530 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): -30.28800 30.52800 ymin,ymax (A): -27.56300 30.66700 zmin,zma (A): 22.18900 87.84100 x,y,z range (A): 60.81600 58.23000 65.65201 scale (grids/A): 0.5422530 object centre (A): 0.1199999 1.552000 55.01500 number of atom coordinates read : 2752 total number of charged atoms : 2616 net assigned charge : 12.00002 assigned positive charge : 407.6815 centred at (gu) : 91.30350 90.65656 91.35141 assigned negative charge : -395.6824 centred at (gu) : 91.28911 90.73657 91.20161 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5272 nv = 96 ne = 84 npr = 52915 no. pairs analyzed = 52915 no. exposed pairs = 4051 no. arc points = 28522 no. surface atoms = 1331 nbur = 1421 mkacc time = 0.1200000 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 = 1.568000 m= 220 mr = 2315 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2828 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.8229321E-11 1.9425159E-09 midg,1,midg; midg,igrid,midg 8.8438007E-10 2.5346239E-10 1,midg,midg; igrid,midg,midg 4.1020379E-10 9.7227182E-10 gauss-seidel spectral radius is 0.9824612 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 17:16:49 rms-change max change #iterations 6.6246346E-02 14.76265 at 10iterations 4.1648033E-03 0.7755804 at 20iterations 2.7245344E-04 4.7966003E-02 at 30iterations 1.8978963E-05 3.4980774E-03 at 40iterations 1.5746244E-06 3.0899048E-04 at 50iterations finished qdiffx linear iterations at : 17:16:52 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.5746244E-06 3.0899048E-04 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 17:16:52 3.679u 0.234s 0:04.24 91.9% 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 Mon Oct 10 2011 at 17:16:53 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 = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.626759 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): -30.28800 30.52800 ymin,ymax (A): -27.56300 30.66700 zmin,zma (A): 22.18900 87.84100 x,y,z range (A): 60.81600 58.23000 65.65201 scale (grids/A): 1.626759 object centre (A): 0.1199999 1.552000 55.01500 number of atom coordinates read : 2752 total number of charged atoms : 2616 net assigned charge : 12.00002 assigned positive charge : 407.6815 centred at (gu) : 93.90962 91.96867 94.05360 assigned negative charge : -395.6824 centred at (gu) : 93.86694 92.20934 93.60453 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28522 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16838 mr = 35457 m= 1816 mr = 10528 m= 55 mr = 779 m= 0 mr = 1 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 0.5000000 number of dielectric boundary points 29414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19984 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) : 0.5422530 object centre at (A) : 0.1199999 1.552000 55.01500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9238614E-02 1.8428098E-02 midg,1,midg; midg,igrid,midg 1.7447637E-02 1.0028873E-02 1,midg,midg; igrid,midg,midg -1.3695108E-03 2.8370777E-03 gauss-seidel spectral radius is 0.9981541 estimated iterations to convergence 185 setup time was (sec) 0.8300000 now iterating at: 17:16:54 rms-change max change #iterations 3.076929 168.2262 at 10iterations 1.257821 54.55885 at 20iterations 0.5183059 20.98358 at 30iterations 0.2124851 9.669880 at 40iterations 8.7734379E-02 3.547478 at 50iterations 3.6224090E-02 1.399745 at 60iterations 1.4986970E-02 0.6064897 at 70iterations 6.1474554E-03 0.2285595 at 80iterations 2.5499051E-03 9.3246460E-02 at 90iterations 1.0510810E-03 4.3533325E-02 at 100iterations 4.3409353E-04 1.6979218E-02 at 110iterations 1.7979399E-04 6.5212250E-03 at 120iterations finished qdiffx linear iterations at : 17:17:01 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 1.7979399E-04 6.5212250E-03 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 17:17:01 8.244u 0.249s 0:08.94 94.8% 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 17:17:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 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: 2.440139 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): -30.28800 30.52800 ymin,ymax (A): -27.56300 30.66700 zmin,zma (A): 22.18900 87.84100 x,y,z range (A): 60.81600 58.23000 65.65201 scale (grids/A): 2.440139 object centre (A): 0.1199999 1.552000 55.01500 number of atom coordinates read : 2752 total number of charged atoms : 2616 net assigned charge : 12.00002 assigned positive charge : 407.6815 centred at (gu) : 95.86420 92.95289 96.08025 assigned negative charge : -395.6824 centred at (gu) : 95.80036 93.31405 95.40672 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 133397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28522 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 57674 mr = 88024 m= 16225 mr = 42898 m= 2850 mr = 11302 m= 255 mr = 1711 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2146 time to turn everything in is 1.140000 number of dielectric boundary points 66377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20900 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) : 1.626759 object centre at (A) : 0.1199999 1.552000 55.01500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3876121 0.3332519 midg,1,midg; midg,igrid,midg 0.2343940 7.9479039E-02 1,midg,midg; igrid,midg,midg 5.7333773E-03 3.6673196E-02 gauss-seidel spectral radius is 0.9991281 estimated iterations to convergence 268 setup time was (sec) 1.470000 now iterating at: 17:17:03 rms-change max change #iterations 8.168733 287.0732 at 10iterations 4.620937 165.9173 at 20iterations 2.593389 67.45209 at 30iterations 1.446081 36.98506 at 40iterations 0.8011133 18.97502 at 50iterations 0.4432446 10.20975 at 60iterations 0.2445603 5.485530 at 70iterations 0.1341849 3.431029 at 80iterations 7.4034259E-02 1.730363 at 90iterations 4.0531013E-02 0.9174399 at 100iterations 2.2261050E-02 0.5154355 at 110iterations 1.2197963E-02 0.2795715 at 120iterations 6.6932798E-03 0.1468663 at 130iterations 3.6628542E-03 9.0573788E-02 at 140iterations 2.0065361E-03 4.3027401E-02 at 150iterations 1.1016261E-03 2.5297165E-02 at 160iterations 6.0270459E-04 1.3057709E-02 at 170iterations 3.3012585E-04 8.6737871E-03 at 180iterations finished qdiffx linear iterations at : 17:17:15 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 3.3012585E-04 8.6737871E-03 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 17:17:16 13.226u 0.254s 0:14.05 95.8% 0+0k 0+0io 0pf+0w