Sat Oct 15 13:37:58 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 15 2011 at 13:38:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 0.6592715 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): 20.40200 67.98700 ymin,ymax (A): 39.24100 93.24000 zmin,zma (A): 44.80800 95.82600 x,y,z range (A): 47.58500 53.99900 51.01799 scale (grids/A): 0.6592715 object centre (A): 44.19450 66.24049 70.31700 number of atom coordinates read : 2358 total number of charged atoms : 2209 net assigned charge : -18.99998 assigned positive charge : 358.7575 centred at (gu) : 89.55865 89.84185 89.41555 assigned negative charge : -377.7577 centred at (gu) : 89.42724 89.96258 89.59119 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7040 nv = 96 ne = 84 npr = 46674 no. pairs analyzed = 46674 no. exposed pairs = 3268 no. arc points = 23899 no. surface atoms = 1080 nbur = 1278 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 418 mr = 3577 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 93 time to turn everything in is 0.3300000 number of dielectric boundary points 3848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8157 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6429389E-08 -7.2073220E-08 midg,1,midg; midg,igrid,midg -2.5648321E-08 -6.8292586E-08 1,midg,midg; igrid,midg,midg -7.9506584E-08 -2.1097209E-08 gauss-seidel spectral radius is 0.9880660 estimated iterations to convergence 75 setup time was (sec) 0.6000000 now iterating at: 13:38:06 rms-change max change #iterations 0.1620325 37.52354 at 10iterations 1.6843768E-02 2.906052 at 20iterations 1.7991250E-03 0.2704887 at 30iterations 1.9093871E-04 2.8793335E-02 at 40iterations 1.9913105E-05 2.9773712E-03 at 50iterations finished qdiffx linear iterations at : 13:38:16 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.9913105E-05 2.9773712E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 13:38:19 3.983u 0.171s 0:18.02 23.0% 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 Sat Oct 15 2011 at 13:38:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 1.977814 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): 20.40200 67.98700 ymin,ymax (A): 39.24100 93.24000 zmin,zma (A): 44.80800 95.82600 x,y,z range (A): 47.58500 53.99900 51.01799 scale (grids/A): 1.977814 object centre (A): 44.19450 66.24049 70.31700 number of atom coordinates read : 2358 total number of charged atoms : 2209 net assigned charge : -18.99998 assigned positive charge : 358.7575 centred at (gu) : 88.67575 89.52522 88.24628 assigned negative charge : -377.7577 centred at (gu) : 88.28148 89.88746 88.77332 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23899 grid for indexing accessible points = 1.400000 m= 26525 mr = 48994 m= 4054 mr = 18722 m= 220 mr = 2328 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2207 time to turn everything in is 0.6600000 number of dielectric boundary points 35534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 17488 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) : 0.6592715 object centre at (A) : 44.19450 66.24049 70.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6002140E-03 -5.5935245E-02 midg,1,midg; midg,igrid,midg -0.1386667 -0.1405749 1,midg,midg; igrid,midg,midg -4.0723115E-02 -2.2590980E-03 gauss-seidel spectral radius is 0.9987210 estimated iterations to convergence 221 setup time was (sec) 1.000000 now iterating at: 13:38:31 rms-change max change #iterations 4.487257 193.9572 at 10iterations 2.139117 80.70107 at 20iterations 1.017834 33.86378 at 30iterations 0.4882232 15.46544 at 40iterations 0.2334118 7.568748 at 50iterations 0.1118192 3.627459 at 60iterations 5.3532954E-02 1.736237 at 70iterations 2.5553506E-02 0.7764130 at 80iterations 1.2234791E-02 0.3923035 at 90iterations 5.8569442E-03 0.1894588 at 100iterations 2.8024092E-03 8.5742950E-02 at 110iterations 1.3410103E-03 4.6045303E-02 at 120iterations finished qdiffx linear iterations at : 13:38:59 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 1.3410103E-03 4.6045303E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 13:39:04 9.650u 0.178s 0:39.02 25.1% 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 15 2011 at 13:39:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 2.966722 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): 20.40200 67.98700 ymin,ymax (A): 39.24100 93.24000 zmin,zma (A): 44.80800 95.82600 x,y,z range (A): 47.58500 53.99900 51.01799 scale (grids/A): 2.966722 object centre (A): 44.19450 66.24049 70.31700 number of atom coordinates read : 2358 total number of charged atoms : 2209 net assigned charge : -18.99998 assigned positive charge : 358.7575 centred at (gu) : 88.01346 89.28779 87.36944 assigned negative charge : -377.7577 centred at (gu) : 87.42214 89.83117 88.15990 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 172834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23899 grid for indexing accessible points = 1.400000 m= 84877 mr = 119333 m= 30530 mr = 67498 m= 7161 mr = 23759 m= 962 mr = 5058 m= 77 mr = 596 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 7544 time to turn everything in is 1.750000 number of dielectric boundary points 80177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 17672 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) : 1.977814 object centre at (A) : 44.19450 66.24049 70.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1871007 -0.7834405 midg,1,midg; midg,igrid,midg -1.834701 -1.208127 1,midg,midg; igrid,midg,midg -0.2756954 3.7522729E-02 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 2.110000 now iterating at: 13:39:13 rms-change max change #iterations 10.33748 363.7238 at 10iterations 6.023006 133.9647 at 20iterations 3.497197 76.45927 at 30iterations 2.028931 43.45953 at 40iterations 1.177063 22.63175 at 50iterations 0.6818575 12.23111 at 60iterations 0.3952715 8.389330 at 70iterations 0.2279158 4.279596 at 80iterations 0.1321008 2.428941 at 90iterations 7.6258697E-02 1.598312 at 100iterations 4.4061169E-02 0.7891784 at 110iterations 2.5528923E-02 0.4844728 at 120iterations 1.4719669E-02 0.2417660 at 130iterations 8.5338699E-03 0.1572701 at 140iterations 4.9223080E-03 9.4254971E-02 at 150iterations 2.8423942E-03 5.1268578E-02 at 160iterations 1.6424825E-03 3.1547546E-02 at 170iterations 9.5327222E-04 1.8596649E-02 at 180iterations finished qdiffx linear iterations at : 13:39:47 total time elapsed so far: 14.65000 # loops : 180 mean,max change (kT/e) : 9.5327222E-04 1.8596649E-02 energy calculations done at 14.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.88000 DelPhi exited at 13:39:48 14.877u 0.183s 0:42.89 35.0% 0+0k 0+0io 0pf+0w