Mon Oct 10 18:50:24 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 Mon Oct 10 2011 at 18:50:24 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 0.6489600 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): 46.80600 101.3990 ymin,ymax (A): 14.09300 68.95000 zmin,zma (A): 20.90200 64.56100 x,y,z range (A): 54.59300 54.85700 43.65900 scale (grids/A): 0.6489600 object centre (A): 74.10250 41.52150 42.73150 number of atom coordinates read : 2101 total number of charged atoms : 1966 net assigned charge : 2.500003 assigned positive charge : 313.8384 centred at (gu) : 89.33353 89.00428 90.92686 assigned negative charge : -311.3389 centred at (gu) : 89.25748 89.08841 91.04063 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6075 nv = 96 ne = 84 npr = 41690 no. pairs analyzed = 41690 no. exposed pairs = 2926 no. arc points = 20488 no. surface atoms = 974 nbur = 1127 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3125 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1935 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4916491E-08 -1.0928868E-08 midg,1,midg; midg,igrid,midg 1.8171082E-08 -4.2277706E-09 1,midg,midg; igrid,midg,midg -5.0263522E-09 1.1952230E-08 gauss-seidel spectral radius is 0.9876581 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 18:50:24 rms-change max change #iterations 0.1386916 25.29143 at 10iterations 1.4089257E-02 2.169806 at 20iterations 1.4728602E-03 0.2095041 at 30iterations 1.9680864E-04 3.8362503E-02 at 40iterations 4.1647341E-05 7.8887939E-03 at 50iterations finished qdiffx linear iterations at : 18:50:27 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.1647341E-05 7.8887939E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 18:50:28 3.393u 0.156s 0:03.86 91.7% 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 Mon Oct 10 2011 at 18:50:28 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 1.946880 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): 46.80600 101.3990 ymin,ymax (A): 14.09300 68.95000 zmin,zma (A): 20.90200 64.56100 x,y,z range (A): 54.59300 54.85700 43.65900 scale (grids/A): 1.946880 object centre (A): 74.10250 41.52150 42.73150 number of atom coordinates read : 2101 total number of charged atoms : 1966 net assigned charge : 2.500003 assigned positive charge : 313.8384 centred at (gu) : 88.00027 87.01257 92.78042 assigned negative charge : -311.3389 centred at (gu) : 87.77232 87.26520 93.12173 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20488 grid for indexing accessible points = 1.400000 m= 24406 mr = 43042 m= 4500 mr = 17516 m= 305 mr = 2711 m= 4 mr = 101 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 0.3400000 number of dielectric boundary points 30286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 15499 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) : 0.6489600 object centre at (A) : 74.10250 41.52150 42.73150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6363177E-02 -9.2813270E-03 midg,1,midg; midg,igrid,midg 2.6751314E-03 5.1411502E-03 1,midg,midg; igrid,midg,midg -1.1928368E-02 4.7258820E-02 gauss-seidel spectral radius is 0.9986527 estimated iterations to convergence 216 setup time was (sec) 0.5500000 now iterating at: 18:50:28 rms-change max change #iterations 3.941045 213.1058 at 10iterations 1.843628 73.41853 at 20iterations 0.8629259 31.47023 at 30iterations 0.4061443 13.63341 at 40iterations 0.1911738 6.402575 at 50iterations 8.9967154E-02 2.952784 at 60iterations 4.2132709E-02 1.635302 at 70iterations 1.9834515E-02 0.7267418 at 80iterations 9.3442509E-03 0.3133049 at 90iterations 4.4011949E-03 0.1439095 at 100iterations 2.0763299E-03 6.6459656E-02 at 110iterations 9.8495476E-04 3.4564972E-02 at 120iterations finished qdiffx linear iterations at : 18:50:36 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 9.8495476E-04 3.4564972E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 18:50:36 7.750u 0.204s 0:08.51 93.4% 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 Mon Oct 10 2011 at 18:50:36 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 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: 2.920320 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): 46.80600 101.3990 ymin,ymax (A): 14.09300 68.95000 zmin,zma (A): 20.90200 64.56100 x,y,z range (A): 54.59300 54.85700 43.65900 scale (grids/A): 2.920320 object centre (A): 74.10250 41.52150 42.73150 number of atom coordinates read : 2101 total number of charged atoms : 1966 net assigned charge : 2.500003 assigned positive charge : 313.8384 centred at (gu) : 87.00025 85.51882 94.17045 assigned negative charge : -311.3389 centred at (gu) : 86.65835 85.89772 94.68260 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20488 grid for indexing accessible points = 1.400000 m= 76279 mr = 104662 m= 30142 mr = 61074 m= 8176 mr = 23739 m= 1325 mr = 5914 m= 93 mr = 860 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 68379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 15727 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) : 1.946880 object centre at (A) : 74.10250 41.52150 42.73150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2048901 -0.1116677 midg,1,midg; midg,igrid,midg -2.0268744E-02 0.2765157 1,midg,midg; igrid,midg,midg -0.3157496 0.9228575 gauss-seidel spectral radius is 0.9992601 estimated iterations to convergence 290 setup time was (sec) 1.100000 now iterating at: 18:50:38 rms-change max change #iterations 9.333267 509.1357 at 10iterations 5.467006 127.4822 at 20iterations 3.182049 84.41197 at 30iterations 1.855681 38.04442 at 40iterations 1.077247 25.38927 at 50iterations 0.6213740 12.28187 at 60iterations 0.3592260 7.199092 at 70iterations 0.2070849 3.900503 at 80iterations 0.1194073 2.333264 at 90iterations 6.8749100E-02 1.331909 at 100iterations 3.9484721E-02 0.7682228 at 110iterations 2.2727236E-02 0.4136829 at 120iterations 1.3079828E-02 0.2407703 at 130iterations 7.5263297E-03 0.1431484 at 140iterations 4.3217838E-03 8.5554123E-02 at 150iterations 2.4847547E-03 4.6371460E-02 at 160iterations 1.4324134E-03 2.8057098E-02 at 170iterations 8.2404842E-04 1.5052795E-02 at 180iterations finished qdiffx linear iterations at : 18:50:49 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 8.2404842E-04 1.5052795E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 18:50:49 12.454u 0.205s 0:12.97 97.5% 0+0k 0+0io 0pf+0w