Sun Oct 9 02:23:24 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 02:23:25 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2074 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7120854 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): -45.06600 4.928000 ymin,ymax (A): 49.39800 88.98300 zmin,zma (A): 23.32700 66.76600 x,y,z range (A): 49.99400 39.58500 43.43900 scale (grids/A): 0.7120854 object centre (A): -20.06900 69.19050 45.04650 number of atom coordinates read : 2074 total number of charged atoms : 1953 net assigned charge : -5.079985 assigned positive charge : 309.6667 centred at (gu) : 90.16951 89.28707 89.10701 assigned negative charge : -314.7471 centred at (gu) : 90.19309 89.26655 89.11613 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7317 nv = 96 ne = 84 npr = 42705 no. pairs analyzed = 42705 no. exposed pairs = 2321 no. arc points = 16278 no. surface atoms = 804 nbur = 1270 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4430 m= 3 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.2700000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1428 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7918 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0371042E-08 -4.4628667E-08 midg,1,midg; midg,igrid,midg -6.7606088E-08 -3.1941759E-08 1,midg,midg; igrid,midg,midg -3.3637068E-08 -6.2728532E-08 gauss-seidel spectral radius is 0.9897191 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 02:23:25 rms-change max change #iterations 0.2098866 25.55139 at 10iterations 2.6577799E-02 3.380855 at 20iterations 3.2706843E-03 0.4905090 at 30iterations 4.1912880E-04 5.6549072E-02 at 40iterations 5.1280331E-05 7.2669983E-03 at 50iterations finished qdiffx linear iterations at : 02:23:28 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.1280331E-05 7.2669983E-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 02:23:28 3.399u 0.204s 0:03.89 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 Sun Oct 9 2011 at 02:23:28 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 # of charge parameter records: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2074 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.136256 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): -45.06600 4.928000 ymin,ymax (A): 49.39800 88.98300 zmin,zma (A): 23.32700 66.76600 x,y,z range (A): 49.99400 39.58500 43.43900 scale (grids/A): 2.136256 object centre (A): -20.06900 69.19050 45.04650 number of atom coordinates read : 2074 total number of charged atoms : 1953 net assigned charge : -5.079985 assigned positive charge : 309.6667 centred at (gu) : 90.50862 87.86115 87.32076 assigned negative charge : -314.7471 centred at (gu) : 90.57930 87.79971 87.34850 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16278 grid for indexing accessible points = 1.400000 m= 32895 mr = 57055 m= 7380 mr = 26082 m= 820 mr = 5521 m= 36 mr = 504 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1102 time to turn everything in is 0.5700000 number of dielectric boundary points 29745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15542 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) : 0.7120854 object centre at (A) : -20.06900 69.19050 45.04650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7415136E-02 -3.2431947E-03 midg,1,midg; midg,igrid,midg -3.6039010E-02 -1.1417131E-02 1,midg,midg; igrid,midg,midg -2.0256544E-02 1.7428180E-02 gauss-seidel spectral radius is 0.9988394 estimated iterations to convergence 232 setup time was (sec) 0.8800000 now iterating at: 02:23:30 rms-change max change #iterations 4.712842 183.4686 at 10iterations 2.343224 79.22692 at 20iterations 1.168244 38.11847 at 30iterations 0.5797356 17.69136 at 40iterations 0.2893257 9.231523 at 50iterations 0.1441340 4.205939 at 60iterations 7.1676575E-02 2.202785 at 70iterations 3.5729524E-02 1.116104 at 80iterations 1.7777758E-02 0.5392528 at 90iterations 8.8455323E-03 0.2682495 at 100iterations 4.4010556E-03 0.1357574 at 110iterations 2.2006803E-03 6.3156128E-02 at 120iterations finished qdiffx linear iterations at : 02:23:36 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.2006803E-03 6.3156128E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 02:23:37 7.744u 0.236s 0:08.27 96.3% 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 Sun Oct 9 2011 at 02:23:37 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2074 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.204384 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): -45.06600 4.928000 ymin,ymax (A): 49.39800 88.98300 zmin,zma (A): 23.32700 66.76600 x,y,z range (A): 49.99400 39.58500 43.43900 scale (grids/A): 3.204384 object centre (A): -20.06900 69.19050 45.04650 number of atom coordinates read : 2074 total number of charged atoms : 1953 net assigned charge : -5.079985 assigned positive charge : 309.6667 centred at (gu) : 90.76283 86.79159 85.98116 assigned negative charge : -314.7471 centred at (gu) : 90.86915 86.69965 86.02269 start vw surface at 0.1300000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179201 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16278 grid for indexing accessible points = 1.400000 m= 100506 mr = 136203 m= 44342 mr = 85881 m= 14520 mr = 38103 m= 3392 mr = 12184 m= 476 mr = 2711 m= 34 mr = 319 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 3868 time to turn everything in is 1.790000 number of dielectric boundary points 67056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 15616 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) : 2.136256 object centre at (A) : -20.06900 69.19050 45.04650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3865809 0.1167431 midg,1,midg; midg,igrid,midg -0.2699121 -6.3960575E-02 1,midg,midg; igrid,midg,midg -0.2394707 0.3770099 gauss-seidel spectral radius is 0.9992925 estimated iterations to convergence 297 setup time was (sec) 2.120000 now iterating at: 02:23:39 rms-change max change #iterations 10.31822 386.7688 at 10iterations 6.026987 135.9875 at 20iterations 3.515028 80.51941 at 30iterations 2.047180 41.49635 at 40iterations 1.192343 28.79362 at 50iterations 0.6952425 11.24609 at 60iterations 0.4040760 7.090570 at 70iterations 0.2361111 3.760628 at 80iterations 0.1373046 2.224201 at 90iterations 7.9897985E-02 1.379879 at 100iterations 4.6508394E-02 0.7607384 at 110iterations 2.7072867E-02 0.4321136 at 120iterations 1.5758330E-02 0.2802658 at 130iterations 9.2000011E-03 0.1578903 at 140iterations 5.3694048E-03 8.9744568E-02 at 150iterations 3.1533770E-03 5.4497719E-02 at 160iterations 1.8542113E-03 3.2377243E-02 at 170iterations 1.1029608E-03 1.8497467E-02 at 180iterations finished qdiffx linear iterations at : 02:23:50 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.1029608E-03 1.8497467E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 02:23:50 12.962u 0.249s 0:13.48 97.9% 0+0k 0+0io 0pf+0w