Sat Oct 8 11:49:26 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+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 8 2011 at 11:49:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4434 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: 0.5694997 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): -27.45900 35.05200 ymin,ymax (A): 35.38400 95.25000 zmin,zma (A): 30.90800 89.44500 x,y,z range (A): 62.51100 59.86600 58.53700 scale (grids/A): 0.5694997 object centre (A): 3.796501 65.31700 60.17650 number of atom coordinates read : 4434 total number of charged atoms : 4274 net assigned charge : -6.499953 assigned positive charge : 668.1669 centred at (gu) : 90.57516 89.07840 89.09309 assigned negative charge : -674.6702 centred at (gu) : 90.44527 89.14559 89.28500 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9077 nv = 96 ne = 84 npr = 93699 no. pairs analyzed = 93699 no. exposed pairs = 4972 no. arc points = 33499 no. surface atoms = 1693 nbur = 2741 mkacc time = 0.2400000 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 = 1.512000 m= 399 mr = 5277 m= 0 mr = 33 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.4700000 number of dielectric boundary points 4166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3451 ## 391 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1773554E-09 -4.5497677E-09 midg,1,midg; midg,igrid,midg 6.5014610E-10 -2.1211517E-09 1,midg,midg; igrid,midg,midg -3.6103995E-09 2.2414610E-09 gauss-seidel spectral radius is 0.9841900 estimated iterations to convergence 65 setup time was (sec) 0.8100000 now iterating at: 11:49:27 rms-change max change #iterations 0.1120422 14.21784 at 10iterations 8.9135403E-03 1.069422 at 20iterations 9.4909314E-04 0.1375885 at 30iterations 2.1385374E-04 2.6884079E-02 at 40iterations 6.8163346E-05 8.6550713E-03 at 50iterations finished qdiffx linear iterations at : 11:49:31 total time elapsed so far: 5.200000 # loops : 50 mean,max change (kT/e) : 6.8163346E-05 8.6550713E-03 energy calculations done at 5.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.380000 DelPhi exited at 11:49:32 5.387u 0.481s 0:06.16 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 8 2011 at 11:49:32 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 = 4434 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: 1.708499 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): -27.45900 35.05200 ymin,ymax (A): 35.38400 95.25000 zmin,zma (A): 30.90800 89.44500 x,y,z range (A): 62.51100 59.86600 58.53700 scale (grids/A): 1.708499 object centre (A): 3.796501 65.31700 60.17650 number of atom coordinates read : 4434 total number of charged atoms : 4274 net assigned charge : -6.499953 assigned positive charge : 668.1669 centred at (gu) : 91.72403 87.23355 87.27770 assigned negative charge : -674.6702 centred at (gu) : 91.33567 87.43615 87.85419 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33499 grid for indexing accessible points = 1.400000 m= 33708 mr = 74355 m= 4108 mr = 24685 m= 110 mr = 2356 m= 0 mr = 20 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5818 time to turn everything in is 0.8300000 number of dielectric boundary points 38630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 33062 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) : 0.5694997 object centre at (A) : 3.796501 65.31700 60.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3275431E-02 -3.1495832E-02 midg,1,midg; midg,igrid,midg 1.9133797E-02 -1.7972982E-02 1,midg,midg; igrid,midg,midg -3.3616077E-02 3.6606446E-02 gauss-seidel spectral radius is 0.9984676 estimated iterations to convergence 203 setup time was (sec) 1.170000 now iterating at: 11:49:34 rms-change max change #iterations 4.651488 186.5068 at 10iterations 2.085573 62.16601 at 20iterations 0.9349778 29.19924 at 30iterations 0.4191142 11.64913 at 40iterations 0.1883901 5.389715 at 50iterations 8.4524080E-02 2.343217 at 60iterations 3.7988488E-02 1.132073 at 70iterations 1.7124632E-02 0.4856873 at 80iterations 7.7165957E-03 0.2227039 at 90iterations 3.5022495E-03 9.7106934E-02 at 100iterations 1.6263289E-03 5.2337646E-02 at 110iterations 7.7040144E-04 2.2476196E-02 at 120iterations finished qdiffx linear iterations at : 11:49:45 total time elapsed so far: 12.77000 # loops : 120 mean,max change (kT/e) : 7.7040144E-04 2.2476196E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 11:49:46 12.920u 0.593s 0:13.81 97.8% 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 Sat Oct 8 2011 at 11:49:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4434 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: 2.562749 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): -27.45900 35.05200 ymin,ymax (A): 35.38400 95.25000 zmin,zma (A): 30.90800 89.44500 x,y,z range (A): 62.51100 59.86600 58.53700 scale (grids/A): 2.562749 object centre (A): 3.796501 65.31700 60.17650 number of atom coordinates read : 4434 total number of charged atoms : 4274 net assigned charge : -6.499953 assigned positive charge : 668.1669 centred at (gu) : 92.58589 85.85004 85.91614 assigned negative charge : -674.6702 centred at (gu) : 92.00331 86.15410 86.78120 start vw surface at 0.1600000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 237536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33499 grid for indexing accessible points = 1.400000 m= 115972 mr = 180608 m= 35557 mr = 95429 m= 6895 mr = 28020 m= 630 mr = 5067 m= 12 mr = 348 m= 0 mr = 2 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 19024 time to turn everything in is 2.150000 number of dielectric boundary points 87128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 34174 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) : 1.708499 object centre at (A) : 3.796501 65.31700 60.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7136206 -0.3654589 midg,1,midg; midg,igrid,midg 0.3213950 -0.2970277 1,midg,midg; igrid,midg,midg -0.3652920 0.4127132 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 2.570000 now iterating at: 11:49:49 rms-change max change #iterations 11.53516 356.4994 at 10iterations 6.728661 144.3684 at 20iterations 3.903047 71.77432 at 30iterations 2.253358 40.58703 at 40iterations 1.298023 22.04103 at 50iterations 0.7481602 12.51273 at 60iterations 0.4284557 7.015820 at 70iterations 0.2459728 4.326884 at 80iterations 0.1409649 2.433686 at 90iterations 8.0639429E-02 1.343304 at 100iterations 4.6094954E-02 0.7308846 at 110iterations 2.6427926E-02 0.4450340 at 120iterations 1.5126550E-02 0.2497587 at 130iterations 8.6856717E-03 0.1759415 at 140iterations 5.0053061E-03 8.1449509E-02 at 150iterations 2.9007443E-03 5.0962448E-02 at 160iterations 1.7050253E-03 2.7074814E-02 at 170iterations 1.0212318E-03 1.8144608E-02 at 180iterations finished qdiffx linear iterations at : 11:50:09 total time elapsed so far: 22.33000 # loops : 180 mean,max change (kT/e) : 1.0212318E-03 1.8144608E-02 energy calculations done at 22.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.50000 DelPhi exited at 11:50:09 22.503u 0.585s 0:23.40 98.6% 0+0k 0+0io 0pf+0w