Sun Oct 9 23:23:44 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 23:23:44 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 = 2212 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: 0.6684943 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): -12.12000 31.32300 ymin,ymax (A): -22.13400 27.47800 zmin,zma (A): -10.54000 42.71400 x,y,z range (A): 43.44300 49.61200 53.25400 scale (grids/A): 0.6684943 object centre (A): 9.601500 2.672000 16.08700 number of atom coordinates read : 2212 total number of charged atoms : 2073 net assigned charge : 1.500009 assigned positive charge : 325.3055 centred at (gu) : 92.15876 91.27346 90.37139 assigned negative charge : -323.8059 centred at (gu) : 92.10872 91.25055 90.07014 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6997 nv = 96 ne = 84 npr = 43028 no. pairs analyzed = 43028 no. exposed pairs = 2945 no. arc points = 20744 no. surface atoms = 988 nbur = 1224 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3749 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1800000 number of dielectric boundary points 3573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4507488E-08 6.8793945E-08 midg,1,midg; midg,igrid,midg -2.3691299E-10 1.1607775E-08 1,midg,midg; igrid,midg,midg -3.7195929E-09 2.2621951E-08 gauss-seidel spectral radius is 0.9883746 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 23:23:45 rms-change max change #iterations 0.1607727 28.30754 at 10iterations 1.7504321E-02 2.543343 at 20iterations 1.9009138E-03 0.2809677 at 30iterations 2.4408840E-04 3.4193039E-02 at 40iterations 5.7890804E-05 1.0305643E-02 at 50iterations finished qdiffx linear iterations at : 23:23:48 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.7890804E-05 1.0305643E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 23:23:48 3.397u 0.187s 0:03.91 91.3% 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 23:23:48 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 = 2212 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: 2.005483 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): -12.12000 31.32300 ymin,ymax (A): -22.13400 27.47800 zmin,zma (A): -10.54000 42.71400 x,y,z range (A): 43.44300 49.61200 53.25400 scale (grids/A): 2.005483 object centre (A): 9.601500 2.672000 16.08700 number of atom coordinates read : 2212 total number of charged atoms : 2073 net assigned charge : 1.500009 assigned positive charge : 325.3055 centred at (gu) : 96.47589 93.82024 91.11413 assigned negative charge : -323.8059 centred at (gu) : 96.32600 93.75154 90.21030 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 74946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20744 grid for indexing accessible points = 1.400000 m= 27404 mr = 51210 m= 4625 mr = 20051 m= 405 mr = 3007 m= 10 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 174 time to turn everything in is 0.3600000 number of dielectric boundary points 32893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 16380 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) : 0.6684943 object centre at (A) : 9.601500 2.672000 16.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7973465E-02 9.5880432E-03 midg,1,midg; midg,igrid,midg 2.1928264E-02 1.8837836E-02 1,midg,midg; igrid,midg,midg -1.3397630E-02 5.5079786E-03 gauss-seidel spectral radius is 0.9987344 estimated iterations to convergence 223 setup time was (sec) 0.5700000 now iterating at: 23:23:49 rms-change max change #iterations 4.233965 171.0087 at 10iterations 2.037975 77.58131 at 20iterations 0.9841288 32.00490 at 30iterations 0.4738321 17.58033 at 40iterations 0.2291826 6.929016 at 50iterations 0.1105490 3.505938 at 60iterations 5.3235669E-02 1.663284 at 70iterations 2.5721220E-02 0.8141565 at 80iterations 1.2380349E-02 0.3903019 at 90iterations 5.9593767E-03 0.1807938 at 100iterations 2.8789891E-03 8.7965012E-02 at 110iterations 1.3947095E-03 4.9934387E-02 at 120iterations finished qdiffx linear iterations at : 23:23:56 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.3947095E-03 4.9934387E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 23:23:57 7.916u 0.210s 0:08.59 94.5% 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 Sun Oct 9 2011 at 23:23:57 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 = 2212 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: 3.008225 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): -12.12000 31.32300 ymin,ymax (A): -22.13400 27.47800 zmin,zma (A): -10.54000 42.71400 x,y,z range (A): 43.44300 49.61200 53.25400 scale (grids/A): 3.008225 object centre (A): 9.601500 2.672000 16.08700 number of atom coordinates read : 2212 total number of charged atoms : 2073 net assigned charge : 1.500009 assigned positive charge : 325.3055 centred at (gu) : 99.71384 95.73036 91.67110 assigned negative charge : -323.8059 centred at (gu) : 99.48896 95.62738 90.31543 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 172640 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20744 grid for indexing accessible points = 1.400000 m= 88115 mr = 123645 m= 32337 mr = 71862 m= 8563 mr = 25903 m= 1717 mr = 6582 m= 190 mr = 1314 m= 3 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 0.9700000 number of dielectric boundary points 74118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16584 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) : 2.005483 object centre at (A) : 9.601500 2.672000 16.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5645474 -6.4655952E-02 midg,1,midg; midg,igrid,midg 0.3526485 9.9054025E-03 1,midg,midg; igrid,midg,midg -0.1688097 4.5803901E-02 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 1.210000 now iterating at: 23:23:58 rms-change max change #iterations 9.901573 359.9980 at 10iterations 5.867448 136.1032 at 20iterations 3.474115 72.90025 at 30iterations 2.049334 47.82263 at 40iterations 1.200973 22.90476 at 50iterations 0.7055685 13.17390 at 60iterations 0.4113948 7.955880 at 70iterations 0.2396413 4.519127 at 80iterations 0.1398950 2.822505 at 90iterations 8.1599154E-02 1.507689 at 100iterations 4.7560845E-02 0.8896427 at 110iterations 2.7695928E-02 0.5168762 at 120iterations 1.6112443E-02 0.2881184 at 130iterations 9.3655055E-03 0.1688690 at 140iterations 5.4512755E-03 0.1045246 at 150iterations 3.1645049E-03 6.0813904E-02 at 160iterations 1.8406615E-03 3.0727386E-02 at 170iterations 1.0707943E-03 1.8976212E-02 at 180iterations finished qdiffx linear iterations at : 23:24:10 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 1.0707943E-03 1.8976212E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 23:24:10 12.742u 0.215s 0:13.22 97.9% 0+0k 0+0io 0pf+0w