Sat Oct 8 23:51:33 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 Sat Oct 8 2011 at 23:51:33 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 = 3472 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-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): -24.08700 37.59100 ymin,ymax (A): 20.29600 79.44800 zmin,zma (A): -34.52600 31.09500 x,y,z range (A): 61.67800 59.15200 65.62100 scale (grids/A): 0.5425093 object centre (A): 6.752000 49.87200 -1.715500 number of atom coordinates read : 3472 total number of charged atoms : 3326 net assigned charge : 11.00004 assigned positive charge : 512.6094 centred at (gu) : 91.74475 89.06416 89.30773 assigned negative charge : -501.6112 centred at (gu) : 91.81031 88.90813 89.28448 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6776 nv = 96 ne = 84 npr = 67579 no. pairs analyzed = 67579 no. exposed pairs = 4800 no. arc points = 33935 no. surface atoms = 1593 nbur = 1879 mkacc time = 0.2000000 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= 280 mr = 3275 m= 0 mr = 9 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3415 ## 449 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4655197E-10 6.4837824E-10 midg,1,midg; midg,igrid,midg -5.4844101E-10 1.2822510E-09 1,midg,midg; igrid,midg,midg 6.8008044E-10 2.6714625E-10 gauss-seidel spectral radius is 0.9825346 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 23:51:34 rms-change max change #iterations 7.5604074E-02 11.99232 at 10iterations 4.8931516E-03 0.7883911 at 20iterations 3.7649853E-04 6.0018539E-02 at 30iterations 5.5397555E-05 7.9023838E-03 at 40iterations 1.3514769E-05 2.4192333E-03 at 50iterations finished qdiffx linear iterations at : 23:51:37 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.3514769E-05 2.4192333E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 23:51:38 4.168u 0.249s 0:04.69 93.8% 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 Sat Oct 8 2011 at 23:51:38 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 = 3472 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-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): -24.08700 37.59100 ymin,ymax (A): 20.29600 79.44800 zmin,zma (A): -34.52600 31.09500 x,y,z range (A): 61.67800 59.15200 65.62100 scale (grids/A): 1.627528 object centre (A): 6.752000 49.87200 -1.715500 number of atom coordinates read : 3472 total number of charged atoms : 3326 net assigned charge : 11.00004 assigned positive charge : 512.6094 centred at (gu) : 95.23334 87.19132 87.92220 assigned negative charge : -501.6112 centred at (gu) : 95.43050 86.72437 87.85295 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 73724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33935 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23696 mr = 47605 m= 2694 mr = 16133 m= 76 mr = 1339 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 257 time to turn everything in is 0.6900000 number of dielectric boundary points 35109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 429 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 25522 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) : 6.752000 49.87200 -1.715500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2973180E-02 2.9352281E-02 midg,1,midg; midg,igrid,midg -1.5289567E-02 8.9965463E-03 1,midg,midg; igrid,midg,midg 7.5999033E-03 6.9272621E-03 gauss-seidel spectral radius is 0.9982364 estimated iterations to convergence 189 setup time was (sec) 0.9900000 now iterating at: 23:51:39 rms-change max change #iterations 3.530821 168.2657 at 10iterations 1.483939 52.79704 at 20iterations 0.6231014 22.93289 at 30iterations 0.2616561 8.814685 at 40iterations 0.1102616 3.792866 at 50iterations 4.6541620E-02 1.731575 at 60iterations 1.9627584E-02 0.6349988 at 70iterations 8.2732150E-03 0.2907000 at 80iterations 3.5078055E-03 0.1226254 at 90iterations 1.4826092E-03 5.2062035E-02 at 100iterations 6.2722212E-04 2.2308350E-02 at 110iterations 2.6715716E-04 8.8768005E-03 at 120iterations finished qdiffx linear iterations at : 23:51:47 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.6715716E-04 8.8768005E-03 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 23:51:48 9.483u 0.281s 0:10.04 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 Sat Oct 8 2011 at 23:51:48 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 = 3472 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-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): -24.08700 37.59100 ymin,ymax (A): 20.29600 79.44800 zmin,zma (A): -34.52600 31.09500 x,y,z range (A): 61.67800 59.15200 65.62100 scale (grids/A): 2.441292 object centre (A): 6.752000 49.87200 -1.715500 number of atom coordinates read : 3472 total number of charged atoms : 3326 net assigned charge : 11.00004 assigned positive charge : 512.6094 centred at (gu) : 97.84975 85.78693 86.88299 assigned negative charge : -501.6112 centred at (gu) : 98.14583 85.08640 86.77959 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 171019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33935 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79613 mr = 117429 m= 24612 mr = 61714 m= 4244 mr = 18606 m= 295 mr = 2745 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 895 time to turn everything in is 1.660000 number of dielectric boundary points 79172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 26570 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) : 6.752000 49.87200 -1.715500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4156025 0.5118995 midg,1,midg; midg,igrid,midg -0.1600731 0.1429141 1,midg,midg; igrid,midg,midg 4.9778402E-02 4.7754485E-02 gauss-seidel spectral radius is 0.9991688 estimated iterations to convergence 274 setup time was (sec) 2.000000 now iterating at: 23:51:50 rms-change max change #iterations 9.294200 368.2208 at 10iterations 5.347439 139.2119 at 20iterations 3.049950 72.85112 at 30iterations 1.727355 41.55372 at 40iterations 0.9722960 19.23908 at 50iterations 0.5462058 10.66689 at 60iterations 0.3064977 5.909584 at 70iterations 0.1711444 3.843523 at 80iterations 9.5606580E-02 1.960497 at 90iterations 5.3428620E-02 1.132043 at 100iterations 2.9757900E-02 0.5898523 at 110iterations 1.6564054E-02 0.3193588 at 120iterations 9.2215864E-03 0.1824442 at 130iterations 5.1197251E-03 0.1019230 at 140iterations 2.8526359E-03 5.3478241E-02 at 150iterations 1.5883506E-03 3.6842346E-02 at 160iterations 8.8238739E-04 1.9485950E-02 at 170iterations 4.8928190E-04 9.3469620E-03 at 180iterations finished qdiffx linear iterations at : 23:52:04 total time elapsed so far: 15.75000 # loops : 180 mean,max change (kT/e) : 4.8928190E-04 9.3469620E-03 energy calculations done at 15.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.93000 DelPhi exited at 23:52:05 15.928u 0.295s 0:16.54 98.0% 0+0k 0+0io 0pf+0w