Tue Oct 11 03:46:46 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 Tue Oct 11 2011 at 03:46:46 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6576881 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): -11.93700 37.28200 ymin,ymax (A): -27.31700 21.37000 zmin,zma (A): -8.710999 45.41800 x,y,z range (A): 49.21900 48.68700 54.12900 scale (grids/A): 0.6576881 object centre (A): 12.67250 -2.973500 18.35350 number of atom coordinates read : 3141 total number of charged atoms : 2729 net assigned charge : -1.298981 assigned positive charge : 437.0606 centred at (gu) : 90.18976 90.97113 91.38320 assigned negative charge : -438.3602 centred at (gu) : 89.92223 90.89190 91.31481 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8371 nv = 96 ne = 84 npr = 59098 no. pairs analyzed = 59098 no. exposed pairs = 3455 no. arc points = 24015 no. surface atoms = 1161 nbur = 1980 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4896 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3500000 number of dielectric boundary points 3937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2281 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9899 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3471460E-08 1.4529452E-08 midg,1,midg; midg,igrid,midg -1.6560540E-08 1.6032505E-08 1,midg,midg; igrid,midg,midg -5.8936312E-08 5.3229265E-08 gauss-seidel spectral radius is 0.9880397 estimated iterations to convergence 75 setup time was (sec) 0.6400000 now iterating at: 03:46:47 rms-change max change #iterations 0.1759996 23.79902 at 10iterations 1.8964166E-02 2.437820 at 20iterations 2.0978975E-03 0.2525387 at 30iterations 2.7400407E-04 3.7559509E-02 at 40iterations 5.6900990E-05 6.4353943E-03 at 50iterations finished qdiffx linear iterations at : 03:46:51 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 5.6900990E-05 6.4353943E-03 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.060000 DelPhi exited at 03:46:52 5.067u 0.419s 0:06.17 88.6% 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 Tue Oct 11 2011 at 03:46:52 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.973064 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): -11.93700 37.28200 ymin,ymax (A): -27.31700 21.37000 zmin,zma (A): -8.710999 45.41800 x,y,z range (A): 49.21900 48.68700 54.12900 scale (grids/A): 1.973064 object centre (A): 12.67250 -2.973500 18.35350 number of atom coordinates read : 3141 total number of charged atoms : 2729 net assigned charge : -1.298981 assigned positive charge : 437.0606 centred at (gu) : 90.56878 92.91301 94.14898 assigned negative charge : -438.3602 centred at (gu) : 89.76614 92.67535 93.94398 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24015 grid for indexing accessible points = 1.400000 m= 35369 mr = 64302 m= 6174 mr = 27128 m= 445 mr = 4063 m= 10 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 836 time to turn everything in is 0.7600000 number of dielectric boundary points 36149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21528 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) : 0.6576881 object centre at (A) : 12.67250 -2.973500 18.35350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4249302E-02 4.7010328E-03 midg,1,midg; midg,igrid,midg -1.4033488E-02 -3.1356285E-03 1,midg,midg; igrid,midg,midg -1.5862025E-02 6.6692255E-02 gauss-seidel spectral radius is 0.9987479 estimated iterations to convergence 224 setup time was (sec) 1.080000 now iterating at: 03:46:54 rms-change max change #iterations 4.897086 199.1608 at 10iterations 2.376993 79.31709 at 20iterations 1.149640 36.05652 at 30iterations 0.5586133 17.35791 at 40iterations 0.2714539 7.928094 at 50iterations 0.1314779 3.711220 at 60iterations 6.3478269E-02 1.733456 at 70iterations 3.0825432E-02 0.8865509 at 80iterations 1.4997367E-02 0.4092064 at 90iterations 7.2768964E-03 0.2139206 at 100iterations 3.5183264E-03 0.1226368 at 110iterations 1.7117586E-03 5.0130844E-02 at 120iterations finished qdiffx linear iterations at : 03:47:05 total time elapsed so far: 12.08000 # loops : 120 mean,max change (kT/e) : 1.7117586E-03 5.0130844E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 03:47:05 12.255u 0.517s 0:13.32 95.7% 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 Tue Oct 11 2011 at 03:47:05 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.959596 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): -11.93700 37.28200 ymin,ymax (A): -27.31700 21.37000 zmin,zma (A): -8.710999 45.41800 x,y,z range (A): 49.21900 48.68700 54.12900 scale (grids/A): 2.959596 object centre (A): 12.67250 -2.973500 18.35350 number of atom coordinates read : 3141 total number of charged atoms : 2729 net assigned charge : -1.298981 assigned positive charge : 437.0606 centred at (gu) : 90.85313 94.36940 96.22334 assigned negative charge : -438.3602 centred at (gu) : 89.64909 94.01296 95.91585 start vw surface at 0.1400000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 207596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24015 grid for indexing accessible points = 1.400000 m= 111756 mr = 155038 m= 43908 mr = 93550 m= 11437 mr = 36160 m= 1835 mr = 8879 m= 171 mr = 1280 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 2895 time to turn everything in is 2.040000 number of dielectric boundary points 81727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 21832 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) : 1.973064 object centre at (A) : 12.67250 -2.973500 18.35350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2829108 0.2499064 midg,1,midg; midg,igrid,midg -0.1622756 1.1667497E-02 1,midg,midg; igrid,midg,midg -6.7683518E-02 0.5844505 gauss-seidel spectral radius is 0.9992859 estimated iterations to convergence 295 setup time was (sec) 2.430000 now iterating at: 03:47:08 rms-change max change #iterations 11.16291 442.6775 at 10iterations 6.551662 153.2485 at 20iterations 3.841683 75.75671 at 30iterations 2.246080 41.33817 at 40iterations 1.314234 25.40688 at 50iterations 0.7664961 14.11956 at 60iterations 0.4478761 7.449997 at 70iterations 0.2604451 4.704578 at 80iterations 0.1517332 2.875692 at 90iterations 8.8479504E-02 1.437180 at 100iterations 5.1478621E-02 0.9304271 at 110iterations 3.0020561E-02 0.5706863 at 120iterations 1.7523820E-02 0.2906051 at 130iterations 1.0251067E-02 0.1686592 at 140iterations 6.0101240E-03 9.8535538E-02 at 150iterations 3.5579107E-03 5.6270599E-02 at 160iterations 2.1246606E-03 3.6499023E-02 at 170iterations 1.2908644E-03 2.4879456E-02 at 180iterations finished qdiffx linear iterations at : 03:47:27 total time elapsed so far: 21.35000 # loops : 180 mean,max change (kT/e) : 1.2908644E-03 2.4879456E-02 energy calculations done at 21.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.52000 DelPhi exited at 03:47:28 21.521u 0.518s 0:22.66 97.2% 0+0k 0+0io 0pf+0w