Sat Oct 8 11:44:46 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 11:44:46 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 = 5441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5337332 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): 11.78800 76.61900 ymin,ymax (A): -26.77300 39.41200 zmin,zma (A): 76.36800 143.0680 x,y,z range (A): 64.83099 66.18500 66.69999 scale (grids/A): 0.5337332 object centre (A): 44.20350 6.319502 109.7180 number of atom coordinates read : 5441 total number of charged atoms : 5271 net assigned charge : 1.000028 assigned positive charge : 828.5482 centred at (gu) : 89.78751 89.69141 90.73158 assigned negative charge : -827.5544 centred at (gu) : 89.82352 89.69499 90.75263 start vw surface at 0.2700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 9571 nv = 96 ne = 84 npr = 113477 no. pairs analyzed = 113477 no. exposed pairs = 6392 no. arc points = 43604 no. surface atoms = 2140 nbur = 3301 mkacc time = 0.3300000 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= 368 mr = 5225 m= 0 mr = 13 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 4701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4356 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 12937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6705252E-10 -1.5126031E-10 midg,1,midg; midg,igrid,midg 7.1582545E-11 1.0130063E-11 1,midg,midg; igrid,midg,midg 3.3387346E-10 -2.2874157E-10 gauss-seidel spectral radius is 0.9820797 estimated iterations to convergence 62 setup time was (sec) 0.9300000 now iterating at: 11:44:48 rms-change max change #iterations 9.1447584E-02 12.07513 at 10iterations 7.3622842E-03 1.390114 at 20iterations 1.3000818E-03 0.3201065 at 30iterations 3.3705967E-04 7.8536987E-02 at 40iterations 9.3454604E-05 2.0111084E-02 at 50iterations finished qdiffx linear iterations at : 11:44:51 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 9.3454604E-05 2.0111084E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 11:44:51 4.305u 0.199s 0:04.82 93.1% 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 8 2011 at 11:44:51 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 = 5441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.601200 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): 11.78800 76.61900 ymin,ymax (A): -26.77300 39.41200 zmin,zma (A): 76.36800 143.0680 x,y,z range (A): 64.83099 66.18500 66.69999 scale (grids/A): 1.601200 object centre (A): 44.20350 6.319502 109.7180 number of atom coordinates read : 5441 total number of charged atoms : 5271 net assigned charge : 1.000028 assigned positive charge : 828.5482 centred at (gu) : 89.36063 89.07254 92.19339 assigned negative charge : -827.5544 centred at (gu) : 89.47012 89.08464 92.25750 start vw surface at 0.2700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 108582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43604 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32880 mr = 76926 m= 3268 mr = 22509 m= 82 mr = 1561 m= 0 mr = 3 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1039 time to turn everything in is 0.9500000 number of dielectric boundary points 43813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 524 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 40177 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) : 0.5337332 object centre at (A) : 44.20350 6.319502 109.7180 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2300750E-02 8.9143841E-03 midg,1,midg; midg,igrid,midg 1.3941403E-02 -2.6954769E-03 1,midg,midg; igrid,midg,midg 1.6063963E-03 -7.8342166E-03 gauss-seidel spectral radius is 0.9983402 estimated iterations to convergence 195 setup time was (sec) 1.330000 now iterating at: 11:44:53 rms-change max change #iterations 4.533878 166.1293 at 10iterations 1.965430 69.65299 at 20iterations 0.8513021 23.88573 at 30iterations 0.3704473 10.32024 at 40iterations 0.1612599 5.002587 at 50iterations 6.9981001E-02 2.018906 at 60iterations 3.0559529E-02 0.8419678 at 70iterations 1.3395145E-02 0.3967113 at 80iterations 5.9218472E-03 0.1968002 at 90iterations 2.6593301E-03 8.5487366E-02 at 100iterations 1.2246800E-03 4.4487000E-02 at 110iterations 5.8710988E-04 2.1881104E-02 at 120iterations finished qdiffx linear iterations at : 11:45:02 total time elapsed so far: 10.24000 # loops : 120 mean,max change (kT/e) : 5.8710988E-04 2.1881104E-02 energy calculations done at 10.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 11:45:02 10.483u 0.232s 0:10.99 97.4% 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 Sat Oct 8 2011 at 11:45:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2000000 grid size : 179 scale,in grids/A, set to be: 2.401799 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): 11.78800 76.61900 ymin,ymax (A): -26.77300 39.41200 zmin,zma (A): 76.36800 143.0680 x,y,z range (A): 64.83099 66.18500 66.69999 scale (grids/A): 2.401799 object centre (A): 44.20350 6.319502 109.7180 number of atom coordinates read : 5441 total number of charged atoms : 5271 net assigned charge : 1.000028 assigned positive charge : 828.5482 centred at (gu) : 89.04065 88.60833 93.28977 assigned negative charge : -827.5544 centred at (gu) : 89.20512 88.62674 93.38624 start vw surface at 0.3100000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 253183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43604 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 115828 mr = 188587 m= 31844 mr = 91705 m= 4897 mr = 23751 m= 308 mr = 3151 m= 3 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 3467 time to turn everything in is 2.380000 number of dielectric boundary points 98756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 2.550000 number of grid points assigned charge 42117 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) : 1.601200 object centre at (A) : 44.20350 6.319502 109.7180 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3239626 6.5710284E-02 midg,1,midg; midg,igrid,midg 0.1853633 -6.1225280E-02 1,midg,midg; igrid,midg,midg -6.8408161E-02 -0.1142821 gauss-seidel spectral radius is 0.9992377 estimated iterations to convergence 286 setup time was (sec) 2.750000 now iterating at: 11:45:05 rms-change max change #iterations 11.93041 294.6886 at 10iterations 7.051233 179.7484 at 20iterations 4.141664 103.8245 at 30iterations 2.426307 54.30240 at 40iterations 1.410214 25.70088 at 50iterations 0.8223162 18.96326 at 60iterations 0.4766433 10.66185 at 70iterations 0.2752154 5.123558 at 80iterations 0.1590202 3.068539 at 90iterations 9.1783464E-02 1.773709 at 100iterations 5.2883942E-02 1.012585 at 110iterations 3.0526951E-02 0.6019440 at 120iterations 1.7598528E-02 0.3525524 at 130iterations 1.0168081E-02 0.1970530 at 140iterations 5.8868970E-03 0.1227417 at 150iterations 3.4287488E-03 6.3964844E-02 at 160iterations 2.0131518E-03 4.2366028E-02 at 170iterations 1.2017582E-03 2.0965576E-02 at 180iterations finished qdiffx linear iterations at : 11:45:18 total time elapsed so far: 15.51000 # loops : 180 mean,max change (kT/e) : 1.2017582E-03 2.0965576E-02 energy calculations done at 15.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.75000 DelPhi exited at 11:45:19 15.747u 0.196s 0:16.24 98.0% 0+0k 0+0io 0pf+0w