Mon Oct 10 14:08:20 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+sph2.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 = amb2.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 14:08:20 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5383417 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): -9.565001 47.82000 ymin,ymax (A): -19.33600 35.64300 zmin,zma (A): -24.64800 41.48100 x,y,z range (A): 57.38500 54.97900 66.12901 scale (grids/A): 0.5383417 object centre (A): 19.12750 8.153499 8.416501 number of atom coordinates read : 3291 total number of charged atoms : 3153 net assigned charge : 0.5000058 assigned positive charge : 502.0565 centred at (gu) : 88.33773 87.98504 90.74296 assigned negative charge : -501.5578 centred at (gu) : 88.26479 88.03258 90.62544 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6121 nv = 96 ne = 84 npr = 66987 no. pairs analyzed = 66987 no. exposed pairs = 4396 no. arc points = 30565 no. surface atoms = 1463 nbur = 1828 mkacc time = 0.1500000 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 = 1.596000 m= 244 mr = 2988 m= 0 mr = 6 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3107 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3282168E-10 8.0185175E-10 midg,1,midg; midg,igrid,midg 4.7387572E-10 -1.4795942E-10 1,midg,midg; igrid,midg,midg -5.9897798E-10 2.7723246E-10 gauss-seidel spectral radius is 0.9822414 estimated iterations to convergence 62 setup time was (sec) 0.5800000 now iterating at: 14:08:21 rms-change max change #iterations 7.3461041E-02 12.97166 at 10iterations 4.9185543E-03 0.8247070 at 20iterations 4.3421428E-04 0.1023102 at 30iterations 6.1661027E-05 9.9983215E-03 at 40iterations 1.1139743E-05 1.8787384E-03 at 50iterations finished qdiffx linear iterations at : 14:08:24 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.1139743E-05 1.8787384E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:08:24 3.352u 0.159s 0:03.82 91.6% 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 14:08:24 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3291 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: 1.615025 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): -9.565001 47.82000 ymin,ymax (A): -19.33600 35.64300 zmin,zma (A): -24.64800 41.48100 x,y,z range (A): 57.38500 54.97900 66.12901 scale (grids/A): 1.615025 object centre (A): 19.12750 8.153499 8.416501 number of atom coordinates read : 3291 total number of charged atoms : 3153 net assigned charge : 0.5000058 assigned positive charge : 502.0565 centred at (gu) : 85.01249 83.95438 92.22774 assigned negative charge : -501.5578 centred at (gu) : 84.79414 84.09720 91.87590 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30565 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20075 mr = 45343 m= 2122 mr = 13181 m= 65 mr = 981 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 275 time to turn everything in is 0.4900000 number of dielectric boundary points 31130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 24072 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) : 0.5383417 object centre at (A) : 19.12750 8.153499 8.416501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0648019E-03 2.5718661E-02 midg,1,midg; midg,igrid,midg -8.5184285E-03 -1.0165802E-02 1,midg,midg; igrid,midg,midg -1.4506858E-02 8.1284670E-04 gauss-seidel spectral radius is 0.9981757 estimated iterations to convergence 186 setup time was (sec) 0.7700000 now iterating at: 14:08:25 rms-change max change #iterations 3.473500 161.8358 at 10iterations 1.445719 67.58405 at 20iterations 0.5989217 21.07422 at 30iterations 0.2491178 8.731574 at 40iterations 0.1035653 3.700333 at 50iterations 4.3115716E-02 1.534257 at 60iterations 1.7928207E-02 0.6548395 at 70iterations 7.5006825E-03 0.2718391 at 80iterations 3.1358777E-03 0.1150885 at 90iterations 1.3097672E-03 5.0182343E-02 at 100iterations 5.5226200E-04 1.8943787E-02 at 110iterations 2.3304595E-04 8.1443787E-03 at 120iterations finished qdiffx linear iterations at : 14:08:32 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 2.3304595E-04 8.1443787E-03 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 14:08:32 7.418u 0.222s 0:07.96 95.8% 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 Mon Oct 10 2011 at 14:08:32 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3291 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: 2.422538 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): -9.565001 47.82000 ymin,ymax (A): -19.33600 35.64300 zmin,zma (A): -24.64800 41.48100 x,y,z range (A): 57.38500 54.97900 66.12901 scale (grids/A): 2.422538 object centre (A): 19.12750 8.153499 8.416501 number of atom coordinates read : 3291 total number of charged atoms : 3153 net assigned charge : 0.5000058 assigned positive charge : 502.0565 centred at (gu) : 82.51848 80.93146 93.34146 assigned negative charge : -501.5578 centred at (gu) : 82.19106 81.14552 92.81380 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 158928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30565 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 70438 mr = 111830 m= 19296 mr = 54143 m= 3332 mr = 13757 m= 252 mr = 2155 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 889 time to turn everything in is 1.190000 number of dielectric boundary points 70274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 25189 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) : 1.615025 object centre at (A) : 19.12750 8.153499 8.416501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1607069E-02 0.3195929 midg,1,midg; midg,igrid,midg -0.2147870 -0.1751496 1,midg,midg; igrid,midg,midg -0.1985107 -9.0218219E-04 gauss-seidel spectral radius is 0.9991397 estimated iterations to convergence 269 setup time was (sec) 1.490000 now iterating at: 14:08:34 rms-change max change #iterations 9.104358 302.2242 at 10iterations 5.126634 124.5523 at 20iterations 2.876061 74.72928 at 30iterations 1.598768 33.77336 at 40iterations 0.8895946 18.50197 at 50iterations 0.4926023 10.65954 at 60iterations 0.2722356 5.934959 at 70iterations 0.1499303 3.176319 at 80iterations 8.2722388E-02 1.700159 at 90iterations 4.5555972E-02 1.042155 at 100iterations 2.5106495E-02 0.5232213 at 110iterations 1.3832031E-02 0.2808075 at 120iterations 7.6002008E-03 0.1602274 at 130iterations 4.1898829E-03 8.6671829E-02 at 140iterations 2.3143357E-03 4.6984196E-02 at 150iterations 1.2708050E-03 2.5785446E-02 at 160iterations 7.0263451E-04 1.4450073E-02 at 170iterations 3.8934854E-04 7.7877045E-03 at 180iterations finished qdiffx linear iterations at : 14:08:44 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 3.8934854E-04 7.7877045E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 14:08:45 11.986u 0.221s 0:13.00 93.8% 0+0k 0+0io 0pf+0w