Sat Oct 15 11:52:37 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 15 2011 at 11:52:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6383360 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): -13.14000 39.70900 ymin,ymax (A): -30.48200 25.28800 zmin,zma (A): 3.054000 45.27000 x,y,z range (A): 52.84900 55.77000 42.21600 scale (grids/A): 0.6383360 object centre (A): 13.28450 -2.597000 24.16200 number of atom coordinates read : 2204 total number of charged atoms : 2070 net assigned charge : 8.000023 assigned positive charge : 317.2598 centred at (gu) : 90.91208 91.03101 88.75519 assigned negative charge : -309.2603 centred at (gu) : 90.84528 91.07271 88.87102 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6235 nv = 96 ne = 84 npr = 43729 no. pairs analyzed = 43729 no. exposed pairs = 2990 no. arc points = 21527 no. surface atoms = 995 nbur = 1209 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3146 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2047 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7259 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7465907E-08 5.2468213E-10 midg,1,midg; midg,igrid,midg 1.1764504E-08 8.8672492E-09 1,midg,midg; igrid,midg,midg 4.1588435E-09 2.0366388E-08 gauss-seidel spectral radius is 0.9872630 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 11:52:38 rms-change max change #iterations 0.1317275 20.88900 at 10iterations 1.2639373E-02 1.905453 at 20iterations 1.2146091E-03 0.1774673 at 30iterations 1.2021334E-04 1.9454002E-02 at 40iterations 1.1911276E-05 1.7910004E-03 at 50iterations finished qdiffx linear iterations at : 11:52:41 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1911276E-05 1.7910004E-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) 3.350000 DelPhi exited at 11:52:41 3.357u 0.169s 0:03.84 91.4% 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 15 2011 at 11:52:41 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.915008 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): -13.14000 39.70900 ymin,ymax (A): -30.48200 25.28800 zmin,zma (A): 3.054000 45.27000 x,y,z range (A): 52.84900 55.77000 42.21600 scale (grids/A): 1.915008 object centre (A): 13.28450 -2.597000 24.16200 number of atom coordinates read : 2204 total number of charged atoms : 2070 net assigned charge : 8.000023 assigned positive charge : 317.2598 centred at (gu) : 92.73624 93.09299 86.26553 assigned negative charge : -309.2603 centred at (gu) : 92.53600 93.21824 86.61346 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21527 grid for indexing accessible points = 1.400000 m= 23616 mr = 43644 m= 3676 mr = 16651 m= 234 mr = 2087 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 335 time to turn everything in is 0.3400000 number of dielectric boundary points 31526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 16291 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) : 0.6383360 object centre at (A) : 13.28450 -2.597000 24.16200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0148827E-02 -5.1257112E-03 midg,1,midg; midg,igrid,midg 4.3599341E-02 2.3009289E-02 1,midg,midg; igrid,midg,midg 1.8168423E-02 4.1690107E-02 gauss-seidel spectral radius is 0.9986231 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 11:52:42 rms-change max change #iterations 3.790390 176.6039 at 10iterations 1.761160 67.36066 at 20iterations 0.8207977 26.59505 at 30iterations 0.3799694 12.80874 at 40iterations 0.1772266 5.468493 at 50iterations 8.2385167E-02 2.826005 at 60iterations 3.8446717E-02 1.274210 at 70iterations 1.7899785E-02 0.7593002 at 80iterations 8.3080996E-03 0.2938566 at 90iterations 3.8832189E-03 0.1362462 at 100iterations 1.8135288E-03 6.1340332E-02 at 110iterations 8.4666238E-04 2.6794434E-02 at 120iterations finished qdiffx linear iterations at : 11:52:49 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 8.4666238E-04 2.6794434E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 11:52:50 7.851u 0.203s 0:08.46 95.1% 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 15 2011 at 11:52:50 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 = 2204 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.872512 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): -13.14000 39.70900 ymin,ymax (A): -30.48200 25.28800 zmin,zma (A): 3.054000 45.27000 x,y,z range (A): 52.84900 55.77000 42.21600 scale (grids/A): 2.872512 object centre (A): 13.28450 -2.597000 24.16200 number of atom coordinates read : 2204 total number of charged atoms : 2070 net assigned charge : 8.000023 assigned positive charge : 317.2598 centred at (gu) : 94.10432 94.63945 84.39828 assigned negative charge : -309.2603 centred at (gu) : 93.80405 94.82744 84.92029 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 153509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21527 grid for indexing accessible points = 1.400000 m= 75561 mr = 106408 m= 27536 mr = 60004 m= 6588 mr = 21456 m= 975 mr = 4666 m= 68 mr = 628 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1120 time to turn everything in is 0.8400000 number of dielectric boundary points 71055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 16558 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) : 1.915008 object centre at (A) : 13.28450 -2.597000 24.16200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3130710 -4.4643067E-02 midg,1,midg; midg,igrid,midg 0.6296157 0.3060564 1,midg,midg; igrid,midg,midg 0.2112474 0.4110385 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 1.080000 now iterating at: 11:52:51 rms-change max change #iterations 9.109709 397.6111 at 10iterations 5.372874 200.8183 at 20iterations 3.144125 76.75693 at 30iterations 1.831448 40.79421 at 40iterations 1.066106 25.66175 at 50iterations 0.6165578 13.07277 at 60iterations 0.3562075 7.596449 at 70iterations 0.2054651 4.162964 at 80iterations 0.1183810 2.379904 at 90iterations 6.8577319E-02 1.346690 at 100iterations 3.9537948E-02 0.8319044 at 110iterations 2.2719212E-02 0.4522830 at 120iterations 1.3073151E-02 0.2771225 at 130iterations 7.5025233E-03 0.1544726 at 140iterations 4.3166298E-03 7.9242706E-02 at 150iterations 2.4794952E-03 5.4708779E-02 at 160iterations 1.4242639E-03 2.8697133E-02 at 170iterations 8.1872230E-04 1.6672134E-02 at 180iterations finished qdiffx linear iterations at : 11:53:02 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 8.1872230E-04 1.6672134E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 11:53:03 12.468u 0.207s 0:13.04 97.0% 0+0k 0+0io 0pf+0w