Sun Oct 9 08:49:05 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 Sun Oct 9 2011 at 08:49:05 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5418 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5174268 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): -33.70200 35.10000 ymin,ymax (A): -33.26700 31.44400 zmin,zma (A): -11.41200 52.59900 x,y,z range (A): 68.80200 64.71100 64.01100 scale (grids/A): 0.5174268 object centre (A): 0.6989994 -0.9114990 20.59350 number of atom coordinates read : 5418 total number of charged atoms : 5253 net assigned charge : -1.999972 assigned positive charge : 812.4802 centred at (gu) : 90.01004 88.73774 90.15783 assigned negative charge : -814.4868 centred at (gu) : 90.11650 88.70971 90.24770 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9076 nv = 96 ne = 84 npr = 110200 no. pairs analyzed = 110200 no. exposed pairs = 6970 no. arc points = 47869 no. surface atoms = 2328 nbur = 3090 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 = 1.652000 m= 331 mr = 4599 m= 0 mr = 11 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.5000000 number of dielectric boundary points 4797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4633 ## 650 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0131317E-10 -4.1081938E-10 midg,1,midg; midg,igrid,midg -2.0442802E-10 5.2949551E-11 1,midg,midg; igrid,midg,midg 3.7691084E-10 -4.6240894E-10 gauss-seidel spectral radius is 0.9809412 estimated iterations to convergence 60 setup time was (sec) 0.7300000 now iterating at: 08:49:06 rms-change max change #iterations 7.7836514E-02 14.11111 at 10iterations 4.5763222E-03 0.6603241 at 20iterations 3.9105632E-04 6.2755585E-02 at 30iterations 7.9360441E-05 1.4986992E-02 at 40iterations 2.2577544E-05 3.9825439E-03 at 50iterations finished qdiffx linear iterations at : 08:49:08 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.2577544E-05 3.9825439E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:49:09 3.392u 0.164s 0:03.83 92.6% 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 Sun Oct 9 2011 at 08:49:09 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5418 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.552280 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): -33.70200 35.10000 ymin,ymax (A): -33.26700 31.44400 zmin,zma (A): -11.41200 52.59900 x,y,z range (A): 68.80200 64.71100 64.01100 scale (grids/A): 1.552280 object centre (A): 0.6989994 -0.9114990 20.59350 number of atom coordinates read : 5418 total number of charged atoms : 5253 net assigned charge : -1.999972 assigned positive charge : 812.4802 centred at (gu) : 90.02820 86.21146 90.47164 assigned negative charge : -814.4868 centred at (gu) : 90.34930 86.12869 90.74332 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 29376 mr = 69959 m= 2605 mr = 18905 m= 52 mr = 1082 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1539 time to turn everything in is 0.7000000 number of dielectric boundary points 44676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 620 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 39615 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) : 0.5174268 object centre at (A) : 0.6989994 -0.9114990 20.59350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0956685E-03 -6.0981256E-03 midg,1,midg; midg,igrid,midg -2.0675715E-03 -2.7285377E-03 1,midg,midg; igrid,midg,midg 5.4513607E-03 -2.0889048E-02 gauss-seidel spectral radius is 0.9982294 estimated iterations to convergence 189 setup time was (sec) 0.9700000 now iterating at: 08:49:10 rms-change max change #iterations 4.210733 151.9638 at 10iterations 1.779348 59.84035 at 20iterations 0.7510830 22.89721 at 30iterations 0.3169974 10.11847 at 40iterations 0.1338372 4.138418 at 50iterations 5.6632638E-02 1.618931 at 60iterations 2.3824874E-02 0.6897144 at 70iterations 1.0139745E-02 0.3699722 at 80iterations 4.2711026E-03 0.1304235 at 90iterations 1.8184946E-03 5.3001404E-02 at 100iterations 7.7611028E-04 2.2884846E-02 at 110iterations 3.3241027E-04 9.6827745E-03 at 120iterations finished qdiffx linear iterations at : 08:49:16 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 3.3241027E-04 9.6827745E-03 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 08:49:17 7.494u 0.168s 0:07.95 96.2% 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 08:49:17 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5418 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.328421 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): -33.70200 35.10000 ymin,ymax (A): -33.26700 31.44400 zmin,zma (A): -11.41200 52.59900 x,y,z range (A): 68.80200 64.71100 64.01100 scale (grids/A): 2.328421 object centre (A): 0.6989994 -0.9114990 20.59350 number of atom coordinates read : 5418 total number of charged atoms : 5253 net assigned charge : -1.999972 assigned positive charge : 812.4802 centred at (gu) : 90.04192 84.31667 90.70718 assigned negative charge : -814.4868 centred at (gu) : 90.52386 84.19296 91.11491 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 239162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 105452 mr = 172427 m= 26426 mr = 80716 m= 3679 mr = 18518 m= 197 mr = 2269 m= 2 mr = 53 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 4771 time to turn everything in is 1.670000 number of dielectric boundary points 100936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 41922 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) : 1.552280 object centre at (A) : 0.6989994 -0.9114990 20.59350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2691450 -0.1612029 midg,1,midg; midg,igrid,midg -1.7443333E-02 -3.6199119E-02 1,midg,midg; igrid,midg,midg 5.7625361E-02 -0.5677843 gauss-seidel spectral radius is 0.9992208 estimated iterations to convergence 283 setup time was (sec) 1.960000 now iterating at: 08:49:19 rms-change max change #iterations 11.37479 409.5748 at 10iterations 6.700519 194.6437 at 20iterations 3.918900 91.51819 at 30iterations 2.280823 51.23029 at 40iterations 1.321598 27.29352 at 50iterations 0.7642468 15.70922 at 60iterations 0.4400555 9.272185 at 70iterations 0.2531877 5.216636 at 80iterations 0.1449694 2.986376 at 90iterations 8.3073102E-02 1.650414 at 100iterations 4.7542542E-02 0.8448963 at 110iterations 2.7206065E-02 0.5156884 at 120iterations 1.5506961E-02 0.2688313 at 130iterations 8.8488767E-03 0.1799753 at 140iterations 5.0579328E-03 9.3995214E-02 at 150iterations 2.8927773E-03 4.9968719E-02 at 160iterations 1.6531385E-03 3.1510800E-02 at 170iterations 9.4695488E-04 1.5004188E-02 at 180iterations finished qdiffx linear iterations at : 08:49:29 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 9.4695488E-04 1.5004188E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 08:49:30 12.030u 0.220s 0:12.54 97.6% 0+0k 0+0io 0pf+0w