Sat Oct 8 17:34:26 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 Sat Oct 8 2011 at 17:34:26 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3530 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5243854 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): -2.462000 45.05800 ymin,ymax (A): -30.37100 26.26100 zmin,zma (A): 1.335000 69.22400 x,y,z range (A): 47.52000 56.63200 67.88900 scale (grids/A): 0.5243854 object centre (A): 21.29800 -2.055000 35.27950 number of atom coordinates read : 3530 total number of charged atoms : 3383 net assigned charge : -5.371984 assigned positive charge : 542.2330 centred at (gu) : 90.84655 91.79023 90.58114 assigned negative charge : -547.6069 centred at (gu) : 90.81538 91.74266 90.56952 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6123 nv = 96 ne = 84 npr = 72732 no. pairs analyzed = 72732 no. exposed pairs = 4296 no. arc points = 29267 no. surface atoms = 1466 nbur = 2064 mkacc time = 0.1500000 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 = 1.624000 m= 214 mr = 3211 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3028 ## 449 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5869850E-10 -1.1769442E-10 midg,1,midg; midg,igrid,midg -1.9760844E-10 4.2135163E-11 1,midg,midg; igrid,midg,midg -2.0395073E-10 -4.0346670E-11 gauss-seidel spectral radius is 0.9813007 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 17:34:27 rms-change max change #iterations 6.8845682E-02 11.69587 at 10iterations 4.2714765E-03 0.6867924 at 20iterations 4.6295853E-04 8.7468147E-02 at 30iterations 1.1745450E-04 2.4144173E-02 at 40iterations 3.3995206E-05 6.8378448E-03 at 50iterations finished qdiffx linear iterations at : 17:34:30 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 3.3995206E-05 6.8378448E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:34:30 3.233u 0.157s 0:03.78 89.4% 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 17:34:30 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3530 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.573156 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): -2.462000 45.05800 ymin,ymax (A): -30.37100 26.26100 zmin,zma (A): 1.335000 69.22400 x,y,z range (A): 47.52000 56.63200 67.88900 scale (grids/A): 1.573156 object centre (A): 21.29800 -2.055000 35.27950 number of atom coordinates read : 3530 total number of charged atoms : 3383 net assigned charge : -5.371984 assigned positive charge : 542.2330 centred at (gu) : 92.53869 95.36955 91.74234 assigned negative charge : -547.6069 centred at (gu) : 92.44578 95.22765 91.70808 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29267 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20467 mr = 47361 m= 1918 mr = 13966 m= 37 mr = 856 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 692 time to turn everything in is 0.5000000 number of dielectric boundary points 28753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 388 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 25639 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) : 0.5243854 object centre at (A) : 21.29800 -2.055000 35.27950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7910962E-03 8.2363524E-03 midg,1,midg; midg,igrid,midg -7.2754342E-03 -1.0048516E-02 1,midg,midg; igrid,midg,midg -2.2952987E-03 1.5293460E-04 gauss-seidel spectral radius is 0.9980795 estimated iterations to convergence 181 setup time was (sec) 0.7800000 now iterating at: 17:34:31 rms-change max change #iterations 3.430951 142.3023 at 10iterations 1.391786 49.29502 at 20iterations 0.5670899 19.34227 at 30iterations 0.2316075 9.200764 at 40iterations 9.4180457E-02 3.136592 at 50iterations 3.8343254E-02 1.315473 at 60iterations 1.5693393E-02 0.5587225 at 70iterations 6.4003193E-03 0.2210846 at 80iterations 2.6617392E-03 0.1001301 at 90iterations 1.1233700E-03 3.9922714E-02 at 100iterations 4.9837044E-04 1.8092155E-02 at 110iterations 2.3972406E-04 9.6130371E-03 at 120iterations finished qdiffx linear iterations at : 17:34:37 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 2.3972406E-04 9.6130371E-03 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 17:34:38 6.877u 0.156s 0:07.39 94.9% 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 17:34:38 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3530 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.359734 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): -2.462000 45.05800 ymin,ymax (A): -30.37100 26.26100 zmin,zma (A): 1.335000 69.22400 x,y,z range (A): 47.52000 56.63200 67.88900 scale (grids/A): 2.359734 object centre (A): 21.29800 -2.055000 35.27950 number of atom coordinates read : 3530 total number of charged atoms : 3383 net assigned charge : -5.371984 assigned positive charge : 542.2330 centred at (gu) : 93.80796 98.05422 92.61334 assigned negative charge : -547.6069 centred at (gu) : 93.66850 97.84131 92.56210 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 159582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29267 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72461 mr = 116136 m= 19202 mr = 57363 m= 2766 mr = 14173 m= 168 mr = 1738 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2431 time to turn everything in is 1.160000 number of dielectric boundary points 64720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 27010 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) : 1.573156 object centre at (A) : 21.29800 -2.055000 35.27950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2650646 2.0738309E-02 midg,1,midg; midg,igrid,midg -0.1062519 -0.1482606 1,midg,midg; igrid,midg,midg -3.9265756E-02 3.6418419E-02 gauss-seidel spectral radius is 0.9991105 estimated iterations to convergence 265 setup time was (sec) 1.440000 now iterating at: 17:34:39 rms-change max change #iterations 9.059794 280.0052 at 10iterations 5.024925 123.3672 at 20iterations 2.778964 71.92546 at 30iterations 1.522124 31.43776 at 40iterations 0.8372910 18.10916 at 50iterations 0.4563389 9.344596 at 60iterations 0.2501261 5.574971 at 70iterations 0.1363561 3.027692 at 80iterations 7.4357495E-02 1.430149 at 90iterations 4.0447310E-02 0.8346701 at 100iterations 2.2088120E-02 0.4775983 at 110iterations 1.2042820E-02 0.2593021 at 120iterations 6.5818396E-03 0.1349182 at 130iterations 3.5907745E-03 7.3518753E-02 at 140iterations 1.9688630E-03 4.1830063E-02 at 150iterations 1.0841100E-03 2.2174835E-02 at 160iterations 6.0309784E-04 1.2354851E-02 at 170iterations 3.4176811E-04 6.8789721E-03 at 180iterations finished qdiffx linear iterations at : 17:34:49 total time elapsed so far: 10.78000 # loops : 180 mean,max change (kT/e) : 3.4176811E-04 6.8789721E-03 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 17:34:49 10.961u 0.174s 0:11.42 97.4% 0+0k 0+0io 0pf+0w