Mon Oct 10 16:59:13 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 16:59:14 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 0.5425093 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): -47.50300 2.005000 ymin,ymax (A): -67.20900 -1.588000 zmin,zma (A): -29.37100 19.24400 x,y,z range (A): 49.50800 65.62100 48.61500 scale (grids/A): 0.5425093 object centre (A): -22.74900 -34.39850 -5.063500 number of atom coordinates read : 2647 total number of charged atoms : 2476 net assigned charge : 7.000021 assigned positive charge : 388.5168 centred at (gu) : 90.23621 90.42899 89.45718 assigned negative charge : -381.5177 centred at (gu) : 90.13073 90.25458 89.42406 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5175 nv = 96 ne = 84 npr = 52661 no. pairs analyzed = 52661 no. exposed pairs = 3543 no. arc points = 25292 no. surface atoms = 1192 nbur = 1455 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= 223 mr = 2579 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2521 ## 352 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3859559E-10 4.7456505E-10 midg,1,midg; midg,igrid,midg -4.6129012E-10 1.3705173E-09 1,midg,midg; igrid,midg,midg -1.4832528E-10 9.5225849E-10 gauss-seidel spectral radius is 0.9824643 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 16:59:14 rms-change max change #iterations 6.5317534E-02 10.99824 at 10iterations 4.3408051E-03 0.7650089 at 20iterations 3.4549832E-04 5.5580139E-02 at 30iterations 4.2500011E-05 7.6990128E-03 at 40iterations 7.0795058E-06 1.3809204E-03 at 50iterations finished qdiffx linear iterations at : 16:59:17 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 7.0795058E-06 1.3809204E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 16:59:19 3.676u 0.165s 0:05.10 75.0% 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 16:59:19 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.627528 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): -47.50300 2.005000 ymin,ymax (A): -67.20900 -1.588000 zmin,zma (A): -29.37100 19.24400 x,y,z range (A): 49.50800 65.62100 48.61500 scale (grids/A): 1.627528 object centre (A): -22.74900 -34.39850 -5.063500 number of atom coordinates read : 2647 total number of charged atoms : 2476 net assigned charge : 7.000021 assigned positive charge : 388.5168 centred at (gu) : 90.70818 91.28622 88.37115 assigned negative charge : -381.5177 centred at (gu) : 90.39225 90.76344 88.27223 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 56946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25292 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17897 mr = 37757 m= 1852 mr = 11894 m= 61 mr = 783 m= 0 mr = 8 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 26314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18925 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) : 0.5425093 object centre at (A) : -22.74900 -34.39850 -5.063500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4638278E-04 5.5240127E-03 midg,1,midg; midg,igrid,midg -1.0488204E-02 2.5594093E-02 1,midg,midg; igrid,midg,midg -5.1598619E-03 8.1579313E-03 gauss-seidel spectral radius is 0.9981413 estimated iterations to convergence 184 setup time was (sec) 0.7300000 now iterating at: 16:59:20 rms-change max change #iterations 3.041086 154.9326 at 10iterations 1.254993 52.93668 at 20iterations 0.5172170 20.25293 at 30iterations 0.2135195 8.230957 at 40iterations 8.8361196E-02 3.487387 at 50iterations 3.6386844E-02 1.410591 at 60iterations 1.4976124E-02 0.6009340 at 70iterations 6.2059420E-03 0.2251706 at 80iterations 2.5550749E-03 0.1016798 at 90iterations 1.0608871E-03 4.0847778E-02 at 100iterations 4.3962695E-04 1.7398834E-02 at 110iterations 1.8311842E-04 7.0897341E-03 at 120iterations finished qdiffx linear iterations at : 16:59:27 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.8311842E-04 7.0897341E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 16:59:28 7.829u 0.189s 0:08.64 92.5% 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 Mon Oct 10 2011 at 16:59:28 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 2.441292 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): -47.50300 2.005000 ymin,ymax (A): -67.20900 -1.588000 zmin,zma (A): -29.37100 19.24400 x,y,z range (A): 49.50800 65.62100 48.61500 scale (grids/A): 2.441292 object centre (A): -22.74900 -34.39850 -5.063500 number of atom coordinates read : 2647 total number of charged atoms : 2476 net assigned charge : 7.000021 assigned positive charge : 388.5168 centred at (gu) : 91.06212 91.92916 87.55655 assigned negative charge : -381.5177 centred at (gu) : 90.58830 91.14504 87.40827 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 132205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25292 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61180 mr = 92639 m= 17719 mr = 47649 m= 2719 mr = 12711 m= 179 mr = 1551 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 59391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 19774 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) : 1.627528 object centre at (A) : -22.74900 -34.39850 -5.063500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2156306E-02 6.9730930E-02 midg,1,midg; midg,igrid,midg -0.1357736 0.4170287 1,midg,midg; igrid,midg,midg -6.1728220E-02 0.1048366 gauss-seidel spectral radius is 0.9991217 estimated iterations to convergence 267 setup time was (sec) 1.340000 now iterating at: 16:59:29 rms-change max change #iterations 7.895404 319.5898 at 10iterations 4.411959 157.8507 at 20iterations 2.445927 58.02195 at 30iterations 1.349816 34.22505 at 40iterations 0.7438414 18.03790 at 50iterations 0.4088522 9.250029 at 60iterations 0.2237045 4.848822 at 70iterations 0.1224847 2.655447 at 80iterations 6.7016348E-02 1.423918 at 90iterations 3.6724217E-02 0.9047461 at 100iterations 2.0103604E-02 0.4998360 at 110iterations 1.0933365E-02 0.2488899 at 120iterations 5.9729060E-03 0.1296930 at 130iterations 3.2673378E-03 6.9793701E-02 at 140iterations 1.7834072E-03 4.2696178E-02 at 150iterations 9.7051880E-04 2.0630836E-02 at 160iterations 5.3102960E-04 1.0967493E-02 at 170iterations 2.9032445E-04 6.1111450E-03 at 180iterations finished qdiffx linear iterations at : 16:59:41 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 2.9032445E-04 6.1111450E-03 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 16:59:41 12.936u 0.193s 0:13.47 97.4% 0+0k 0+0io 0pf+0w