Mon Oct 10 09:45:14 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 Mon Oct 10 2011 at 09:45:14 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2829 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5781568 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): 109.8980 171.4730 ymin,ymax (A): -41.00900 11.94300 zmin,zma (A): 46.70900 101.4120 x,y,z range (A): 61.57500 52.95200 54.70300 scale (grids/A): 0.5781568 object centre (A): 140.6855 -14.53300 74.06050 number of atom coordinates read : 2829 total number of charged atoms : 2680 net assigned charge : 7.014014 assigned positive charge : 415.1959 centred at (gu) : 90.15678 88.23826 88.76112 assigned negative charge : -408.1823 centred at (gu) : 90.22834 88.33092 88.63491 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6397 nv = 96 ne = 84 npr = 54868 no. pairs analyzed = 54868 no. exposed pairs = 4305 no. arc points = 30969 no. surface atoms = 1421 nbur = 1408 mkacc time = 0.1200000 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 = 1.456000 m= 308 mr = 2784 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3014 ## 335 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8007 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3631100E-09 2.8368294E-09 midg,1,midg; midg,igrid,midg 4.8018789E-09 -2.0330236E-10 1,midg,midg; igrid,midg,midg 2.6762093E-09 6.8443230E-11 gauss-seidel spectral radius is 0.9845664 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 09:45:14 rms-change max change #iterations 9.5875748E-02 20.81316 at 10iterations 7.2101876E-03 1.105652 at 20iterations 5.3492648E-04 9.7608566E-02 at 30iterations 4.6503304E-05 7.7886581E-03 at 40iterations 6.0045604E-06 1.4085770E-03 at 50iterations finished qdiffx linear iterations at : 09:45:17 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 6.0045604E-06 1.4085770E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 09:45:18 3.091u 0.163s 0:04.02 80.8% 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 Mon Oct 10 2011 at 09:45:18 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2829 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.734470 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): 109.8980 171.4730 ymin,ymax (A): -41.00900 11.94300 zmin,zma (A): 46.70900 101.4120 x,y,z range (A): 61.57500 52.95200 54.70300 scale (grids/A): 1.734470 object centre (A): 140.6855 -14.53300 74.06050 number of atom coordinates read : 2829 total number of charged atoms : 2680 net assigned charge : 7.014014 assigned positive charge : 415.1959 centred at (gu) : 90.46983 84.71407 86.28288 assigned negative charge : -408.1823 centred at (gu) : 90.68462 84.99234 85.90451 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30969 grid for indexing accessible points = 1.400000 m= 22257 mr = 41190 m= 3192 mr = 14463 m= 129 mr = 1676 m= 0 mr = 15 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 36062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 20750 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) : 0.5781568 object centre at (A) : 140.6855 -14.53300 74.06050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5664840E-03 2.7054094E-02 midg,1,midg; midg,igrid,midg 2.3374410E-02 4.9902285E-03 1,midg,midg; igrid,midg,midg 1.7169252E-02 -4.9472717E-03 gauss-seidel spectral radius is 0.9984097 estimated iterations to convergence 199 setup time was (sec) 0.7400000 now iterating at: 09:45:19 rms-change max change #iterations 3.643668 153.1360 at 10iterations 1.605044 68.00093 at 20iterations 0.7026317 28.19278 at 30iterations 0.3100074 10.97393 at 40iterations 0.1360484 4.323944 at 50iterations 5.9717003E-02 2.001240 at 60iterations 2.6289085E-02 0.8954964 at 70iterations 1.1592170E-02 0.4017010 at 80iterations 5.0878562E-03 0.2096128 at 90iterations 2.2437009E-03 7.8628540E-02 at 100iterations 9.8879694E-04 3.9498806E-02 at 110iterations 4.3291826E-04 1.3999939E-02 at 120iterations finished qdiffx linear iterations at : 09:45:25 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 4.3291826E-04 1.3999939E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 09:45:25 6.838u 0.156s 0:07.28 95.8% 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 Mon Oct 10 2011 at 09:45:25 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2829 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.601705 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): 109.8980 171.4730 ymin,ymax (A): -41.00900 11.94300 zmin,zma (A): 46.70900 101.4120 x,y,z range (A): 61.57500 52.95200 54.70300 scale (grids/A): 2.601705 object centre (A): 140.6855 -14.53300 74.06050 number of atom coordinates read : 2829 total number of charged atoms : 2680 net assigned charge : 7.014014 assigned positive charge : 415.1959 centred at (gu) : 90.70457 82.07098 84.42408 assigned negative charge : -408.1823 centred at (gu) : 91.02683 82.48846 83.85658 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 156103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30969 grid for indexing accessible points = 1.400000 m= 71563 mr = 100977 m= 24893 mr = 53862 m= 5404 mr = 18383 m= 523 mr = 3607 m= 25 mr = 236 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 81446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 21427 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) : 1.734470 object centre at (A) : 140.6855 -14.53300 74.06050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1245705 0.3641030 midg,1,midg; midg,igrid,midg 0.3027372 0.1087591 1,midg,midg; igrid,midg,midg 0.2562019 -0.2468348 gauss-seidel spectral radius is 0.9992252 estimated iterations to convergence 284 setup time was (sec) 1.430000 now iterating at: 09:45:27 rms-change max change #iterations 9.248560 265.0292 at 10iterations 5.443758 148.6789 at 20iterations 3.153136 87.39272 at 30iterations 1.818662 42.29773 at 40iterations 1.044793 22.19987 at 50iterations 0.5974471 12.18633 at 60iterations 0.3415145 7.583364 at 70iterations 0.1952369 4.095924 at 80iterations 0.1108982 2.460835 at 90iterations 6.2919728E-02 1.293426 at 100iterations 3.5819076E-02 0.7489624 at 110iterations 2.0326981E-02 0.4094708 at 120iterations 1.1549879E-02 0.2335901 at 130iterations 6.5349154E-03 0.1514797 at 140iterations 3.7112290E-03 7.5015068E-02 at 150iterations 2.1087418E-03 4.2518616E-02 at 160iterations 1.1946644E-03 2.2380829E-02 at 170iterations 6.7668955E-04 1.4280081E-02 at 180iterations finished qdiffx linear iterations at : 09:45:37 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 6.7668955E-04 1.4280081E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 09:45:37 11.369u 0.185s 0:12.27 94.0% 0+0k 0+0io 0pf+0w