Wed Feb 15 08:55:50 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:50 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 = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5526577 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 0.5526577 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2626 net assigned charge : 6.000022 assigned positive charge : 406.4386 centred at (gu) : 90.47396 89.35845 89.24505 assigned negative charge : -400.4397 centred at (gu) : 90.45263 89.21124 89.27933 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 5556 nv = 96 ne = 84 npr = 55542 no. pairs analyzed = 55542 no. exposed pairs = 3808 no. arc points = 26192 no. surface atoms = 1267 nbur = 1498 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 = 1.540000 m= 232 mr = 2714 m= 0 mr = 12 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2680 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7181 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0144270E-10 1.9078238E-10 midg,1,midg; midg,igrid,midg -7.7759349E-10 1.3641266E-09 1,midg,midg; igrid,midg,midg 2.9178568E-10 7.3106710E-10 gauss-seidel spectral radius is 0.9831029 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 08:55:51 rms-change max change #iterations 7.1449816E-02 11.88976 at 10iterations 4.9901437E-03 0.7742634 at 20iterations 4.1999557E-04 6.6558838E-02 at 30iterations 5.7904916E-05 7.9097748E-03 at 40iterations 1.0939762E-05 1.3170242E-03 at 50iterations finished qdiffx linear iterations at : 08:55:54 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.0939762E-05 1.3170242E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:55:55 3.533u 0.166s 0:04.25 86.8% 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 Wed Feb 15 2012 at 08:55:55 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 = 2765 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: 1.657973 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 1.657973 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2626 net assigned charge : 6.000022 assigned positive charge : 406.4386 centred at (gu) : 91.42113 88.07488 87.73470 assigned negative charge : -400.4397 centred at (gu) : 91.35793 87.63366 87.83801 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26192 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18683 mr = 40175 m= 2054 mr = 12355 m= 58 mr = 940 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 28453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 20163 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) : 0.5526577 object centre at (A) : 41.17800 16.03550 30.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3466850E-02 1.6974080E-02 midg,1,midg; midg,igrid,midg -6.7384634E-03 8.9519517E-03 1,midg,midg; igrid,midg,midg 5.3467590E-04 2.2382117E-03 gauss-seidel spectral radius is 0.9982246 estimated iterations to convergence 188 setup time was (sec) 0.7800000 now iterating at: 08:55:56 rms-change max change #iterations 3.271746 151.7495 at 10iterations 1.370516 57.24812 at 20iterations 0.5798022 22.95643 at 30iterations 0.2445611 9.454483 at 40iterations 0.1026613 3.796440 at 50iterations 4.3298446E-02 1.639067 at 60iterations 1.8238239E-02 0.6778011 at 70iterations 7.6934034E-03 0.2862473 at 80iterations 3.2483879E-03 0.1177858 at 90iterations 1.3783318E-03 5.1120758E-02 at 100iterations 5.8630959E-04 2.2025108E-02 at 110iterations 2.5050723E-04 9.5877647E-03 at 120iterations finished qdiffx linear iterations at : 08:56:02 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 2.5050723E-04 9.5877647E-03 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 08:56:05 7.516u 0.207s 0:10.49 73.4% 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 Wed Feb 15 2012 at 08:56:05 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 = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.486960 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 2.486960 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2626 net assigned charge : 6.000022 assigned positive charge : 406.4386 centred at (gu) : 92.13145 87.11221 86.60196 assigned negative charge : -400.4397 centred at (gu) : 92.03682 86.45047 86.75688 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 141860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26192 grid for indexing accessible points = 1.400000 m= 64565 mr = 98875 m= 18507 mr = 49710 m= 3147 mr = 13428 m= 205 mr = 1970 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 64232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 20980 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) : 1.657973 object centre at (A) : 41.17800 16.03550 30.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2987793 0.4451248 midg,1,midg; midg,igrid,midg -5.6764532E-02 0.1460862 1,midg,midg; igrid,midg,midg 1.8123519E-02 1.7286802E-02 gauss-seidel spectral radius is 0.9991554 estimated iterations to convergence 272 setup time was (sec) 1.640000 now iterating at: 08:56:07 rms-change max change #iterations 8.540415 304.4234 at 10iterations 4.901209 174.8094 at 20iterations 2.788346 76.14578 at 30iterations 1.566229 46.33056 at 40iterations 0.8782210 22.05333 at 50iterations 0.4910708 10.93642 at 60iterations 0.2740450 6.634098 at 70iterations 0.1525367 3.370395 at 80iterations 8.4627047E-02 1.967562 at 90iterations 4.6909023E-02 1.019890 at 100iterations 2.6033778E-02 0.5782962 at 110iterations 1.4428729E-02 0.3441982 at 120iterations 7.9874387E-03 0.1777725 at 130iterations 4.4209054E-03 0.1006937 at 140iterations 2.4433488E-03 5.0956011E-02 at 150iterations 1.3523669E-03 2.8022766E-02 at 160iterations 7.4802828E-04 1.5093803E-02 at 170iterations 4.1323126E-04 8.4609985E-03 at 180iterations finished qdiffx linear iterations at : 08:56:19 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 4.1323126E-04 8.4609985E-03 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 08:56:20 13.531u 0.348s 0:14.35 96.6% 0+0k 0+0io 0pf+0w