Sat Oct 8 11:35:29 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 11:35:29 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 = 4326 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: 0.5728262 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): -27.06100 35.08700 ymin,ymax (A): 37.72200 98.08300 zmin,zma (A): 30.81500 90.03100 x,y,z range (A): 62.14799 60.36100 59.21600 scale (grids/A): 0.5728262 object centre (A): 4.013000 67.90250 60.42300 number of atom coordinates read : 4326 total number of charged atoms : 4167 net assigned charge : -2.499949 assigned positive charge : 646.5955 centred at (gu) : 90.67300 87.81583 88.78355 assigned negative charge : -649.0986 centred at (gu) : 90.58248 87.93924 88.95701 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9007 nv = 96 ne = 84 npr = 91356 no. pairs analyzed = 91356 no. exposed pairs = 4920 no. arc points = 33095 no. surface atoms = 1668 nbur = 2658 mkacc time = 0.2400000 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 = 1.484000 m= 390 mr = 5207 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.4800000 number of dielectric boundary points 4163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3452 ## 375 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 11959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9749662E-09 -3.7500953E-09 midg,1,midg; midg,igrid,midg 4.2554724E-09 -2.2124811E-09 1,midg,midg; igrid,midg,midg -2.4388553E-09 1.9818316E-09 gauss-seidel spectral radius is 0.9843675 estimated iterations to convergence 66 setup time was (sec) 0.7900000 now iterating at: 11:35:30 rms-change max change #iterations 0.1133641 19.84435 at 10iterations 9.0613039E-03 1.280528 at 20iterations 1.1496090E-03 0.1759796 at 30iterations 2.8206527E-04 4.4101715E-02 at 40iterations 9.0268186E-05 1.1363983E-02 at 50iterations finished qdiffx linear iterations at : 11:35:35 total time elapsed so far: 5.210000 # loops : 50 mean,max change (kT/e) : 9.0268186E-05 1.1363983E-02 energy calculations done at 5.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.410000 DelPhi exited at 11:35:35 5.410u 0.460s 0:06.21 94.5% 0+0k 0+0io 6pf+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 11:35:35 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 = 4326 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: 1.718479 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): -27.06100 35.08700 ymin,ymax (A): 37.72200 98.08300 zmin,zma (A): 30.81500 90.03100 x,y,z range (A): 62.14799 60.36100 59.21600 scale (grids/A): 1.718479 object centre (A): 4.013000 67.90250 60.42300 number of atom coordinates read : 4326 total number of charged atoms : 4167 net assigned charge : -2.499949 assigned positive charge : 646.5955 centred at (gu) : 92.01748 83.44628 86.34913 assigned negative charge : -649.0986 centred at (gu) : 91.74670 83.81741 86.87041 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 101117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33095 grid for indexing accessible points = 1.400000 m= 34480 mr = 73437 m= 4159 mr = 25297 m= 144 mr = 2463 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6274 time to turn everything in is 0.8500000 number of dielectric boundary points 38681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 32299 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) : 0.5728262 object centre at (A) : 4.013000 67.90250 60.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4278514E-02 -2.4227908E-02 midg,1,midg; midg,igrid,midg 4.1794844E-02 -5.8531491E-03 1,midg,midg; igrid,midg,midg -2.0998983E-02 2.9196016E-02 gauss-seidel spectral radius is 0.9984764 estimated iterations to convergence 203 setup time was (sec) 1.230000 now iterating at: 11:35:37 rms-change max change #iterations 4.593952 158.4510 at 10iterations 2.062410 68.17465 at 20iterations 0.9267599 25.11917 at 30iterations 0.4177243 12.18009 at 40iterations 0.1874106 5.088488 at 50iterations 8.4335290E-02 2.463348 at 60iterations 3.7964102E-02 1.026072 at 70iterations 1.7174991E-02 0.5093532 at 80iterations 7.7674938E-03 0.2200165 at 90iterations 3.5477064E-03 0.1052262 at 100iterations 1.6349274E-03 4.9086571E-02 at 110iterations 7.7287306E-04 2.1631241E-02 at 120iterations finished qdiffx linear iterations at : 11:35:49 total time elapsed so far: 12.84000 # loops : 120 mean,max change (kT/e) : 7.7287306E-04 2.1631241E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 11:35:49 13.014u 0.530s 0:13.91 97.3% 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 Sat Oct 8 2011 at 11:35:49 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 = 4326 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: 2.577718 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): -27.06100 35.08700 ymin,ymax (A): 37.72200 98.08300 zmin,zma (A): 30.81500 90.03100 x,y,z range (A): 62.14799 60.36100 59.21600 scale (grids/A): 2.577718 object centre (A): 4.013000 67.90250 60.42300 number of atom coordinates read : 4326 total number of charged atoms : 4167 net assigned charge : -2.499949 assigned positive charge : 646.5955 centred at (gu) : 93.02586 80.16916 84.52345 assigned negative charge : -649.0986 centred at (gu) : 92.62018 80.72601 85.30564 start vw surface at 0.1600000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 235035 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33095 grid for indexing accessible points = 1.400000 m= 116527 mr = 178158 m= 36685 mr = 95928 m= 7199 mr = 29159 m= 692 mr = 5262 m= 15 mr = 395 m= 0 mr = 4 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 21328 time to turn everything in is 2.140000 number of dielectric boundary points 87247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 33326 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) : 1.718479 object centre at (A) : 4.013000 67.90250 60.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7143851 -0.2901467 midg,1,midg; midg,igrid,midg 0.5921181 -6.7404382E-02 1,midg,midg; igrid,midg,midg -0.2892123 0.2933094 gauss-seidel spectral radius is 0.9992413 estimated iterations to convergence 287 setup time was (sec) 2.590000 now iterating at: 11:35:52 rms-change max change #iterations 11.27674 309.0576 at 10iterations 6.563360 129.5204 at 20iterations 3.796329 72.34497 at 30iterations 2.194138 39.93518 at 40iterations 1.260374 21.52914 at 50iterations 0.7254075 11.92559 at 60iterations 0.4166981 6.968650 at 70iterations 0.2385519 4.064596 at 80iterations 0.1364926 2.165588 at 90iterations 7.8146376E-02 1.375473 at 100iterations 4.4806674E-02 0.7025108 at 110iterations 2.5646117E-02 0.4664001 at 120iterations 1.4684780E-02 0.2366428 at 130iterations 8.4228590E-03 0.1354747 at 140iterations 4.8516919E-03 8.7796211E-02 at 150iterations 2.8128941E-03 5.1265717E-02 at 160iterations 1.6478609E-03 2.6842117E-02 at 170iterations 9.8249293E-04 1.6601563E-02 at 180iterations finished qdiffx linear iterations at : 11:36:12 total time elapsed so far: 22.37000 # loops : 180 mean,max change (kT/e) : 9.8249293E-04 1.6601563E-02 energy calculations done at 22.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.54000 DelPhi exited at 11:36:13 22.541u 0.596s 0:23.61 97.9% 0+0k 0+0io 0pf+0w