Wed Feb 15 08:55:28 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 08:55:28 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: CYM 212 has a net charge of -0.8000 !!! WARNING: ZN 760 has a net charge of 1.6000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5780159 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): -30.96300 30.62700 ymin,ymax (A): 8.261000 56.74400 zmin,zma (A): 37.68700 97.14400 x,y,z range (A): 61.59000 48.48300 59.45700 scale (grids/A): 0.5780159 object centre (A): -0.1680012 32.50250 67.41550 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 14.00001 assigned positive charge : 382.2677 centred at (gu) : 88.36288 90.46062 88.99625 assigned negative charge : -368.2685 centred at (gu) : 88.47687 90.48906 89.06579 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5650 nv = 96 ne = 84 npr = 50150 no. pairs analyzed = 50150 no. exposed pairs = 3411 no. arc points = 24665 no. surface atoms = 1142 nbur = 1396 mkacc time = 0.1300000 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 = 1.512000 m= 244 mr = 2736 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2561 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0126654E-09 1.2904284E-09 midg,1,midg; midg,igrid,midg 2.9522387E-09 2.5649427E-09 1,midg,midg; igrid,midg,midg 6.9134072E-09 6.0162125E-10 gauss-seidel spectral radius is 0.9845229 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 08:55:29 rms-change max change #iterations 8.5851729E-02 14.14983 at 10iterations 6.5838187E-03 1.030769 at 20iterations 5.1410269E-04 8.5749626E-02 at 30iterations 4.3568325E-05 7.2669983E-03 at 40iterations 4.6302898E-06 6.9189072E-04 at 50iterations finished qdiffx linear iterations at : 08:55:31 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.6302898E-06 6.9189072E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:55:32 3.387u 0.161s 0:04.04 87.6% 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 Wed Feb 15 2012 at 08:55:32 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: CYM 212 has a net charge of -0.8000 !!! WARNING: ZN 760 has a net charge of 1.6000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.734048 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): -30.96300 30.62700 ymin,ymax (A): 8.261000 56.74400 zmin,zma (A): 37.68700 97.14400 x,y,z range (A): 61.59000 48.48300 59.45700 scale (grids/A): 1.734048 object centre (A): -0.1680012 32.50250 67.41550 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 14.00001 assigned positive charge : 382.2677 centred at (gu) : 85.08788 91.38120 86.98824 assigned negative charge : -368.2685 centred at (gu) : 85.43019 91.46709 87.19714 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24665 grid for indexing accessible points = 1.400000 m= 19309 mr = 40677 m= 2252 mr = 12879 m= 87 mr = 1116 m= 0 mr = 13 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 0.5100000 number of dielectric boundary points 29123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18608 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) : 0.5780159 object centre at (A) : -0.1680012 32.50250 67.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9285243E-02 2.0541394E-02 midg,1,midg; midg,igrid,midg 1.0707964E-02 1.7365772E-02 1,midg,midg; igrid,midg,midg 2.7011698E-02 8.2419626E-03 gauss-seidel spectral radius is 0.9983543 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 08:55:33 rms-change max change #iterations 3.418459 185.4813 at 10iterations 1.472722 57.44035 at 20iterations 0.6403630 28.79910 at 30iterations 0.2775493 11.90542 at 40iterations 0.1203667 4.839497 at 50iterations 5.2102506E-02 1.907337 at 60iterations 2.2644740E-02 0.8111410 at 70iterations 9.7868899E-03 0.3779774 at 80iterations 4.2517763E-03 0.1653824 at 90iterations 1.8521538E-03 6.8542480E-02 at 100iterations 8.0461730E-04 2.9837608E-02 at 110iterations 3.4972647E-04 1.3532639E-02 at 120iterations finished qdiffx linear iterations at : 08:55:40 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.4972647E-04 1.3532639E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 08:55:41 7.842u 0.371s 0:08.90 92.2% 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 Wed Feb 15 2012 at 08:55:41 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: CYM 212 has a net charge of -0.8000 !!! WARNING: ZN 760 has a net charge of 1.6000 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: 2.601072 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): -30.96300 30.62700 ymin,ymax (A): 8.261000 56.74400 zmin,zma (A): 37.68700 97.14400 x,y,z range (A): 61.59000 48.48300 59.45700 scale (grids/A): 2.601072 object centre (A): -0.1680012 32.50250 67.41550 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 14.00001 assigned positive charge : 382.2677 centred at (gu) : 82.63157 92.07157 85.48213 assigned negative charge : -368.2685 centred at (gu) : 83.14524 92.20057 85.79565 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 143964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24665 grid for indexing accessible points = 1.400000 m= 65978 mr = 99749 m= 19589 mr = 51260 m= 3570 mr = 14294 m= 332 mr = 2331 m= 11 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1972 time to turn everything in is 1.220000 number of dielectric boundary points 65646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 19186 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) : 1.734048 object centre at (A) : -0.1680012 32.50250 67.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5222726 0.2853718 midg,1,midg; midg,igrid,midg 0.1445159 0.2858223 1,midg,midg; igrid,midg,midg 0.1408073 1.8076768E-02 gauss-seidel spectral radius is 0.9991827 estimated iterations to convergence 276 setup time was (sec) 1.550000 now iterating at: 08:55:43 rms-change max change #iterations 8.649430 299.6630 at 10iterations 4.966754 148.4595 at 20iterations 2.826841 77.56526 at 30iterations 1.594112 36.99582 at 40iterations 0.8960297 19.31345 at 50iterations 0.5057679 11.44102 at 60iterations 0.2828036 6.854229 at 70iterations 0.1587340 3.279050 at 80iterations 8.8718094E-02 1.868858 at 90iterations 4.9593702E-02 1.107517 at 100iterations 2.7716622E-02 0.5843201 at 110iterations 1.5475366E-02 0.3279686 at 120iterations 8.6457003E-03 0.2082520 at 130iterations 4.8168409E-03 0.1109009 at 140iterations 2.6847865E-03 5.9128761E-02 at 150iterations 1.4990458E-03 3.0883789E-02 at 160iterations 8.3751598E-04 1.7048120E-02 at 170iterations 4.6627241E-04 9.8443031E-03 at 180iterations finished qdiffx linear iterations at : 08:55:54 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 4.6627241E-04 9.8443031E-03 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 08:55:55 13.018u 0.209s 0:13.81 95.6% 0+0k 0+0io 0pf+0w