Sat Oct 8 11:35:08 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 11:35:08 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4284 !!! WARNING: HIQ 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5847473 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): -25.46900 35.41200 ymin,ymax (A): 38.07700 97.66900 zmin,zma (A): 30.82600 90.66400 x,y,z range (A): 60.88100 59.59200 59.83800 scale (grids/A): 0.5847473 object centre (A): 4.971501 67.87300 60.74500 number of atom coordinates read : 4284 total number of charged atoms : 4126 net assigned charge : -0.9859650 assigned positive charge : 642.9156 centred at (gu) : 90.57969 88.16360 88.43948 assigned negative charge : -643.9046 centred at (gu) : 90.45674 88.31570 88.57300 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9249 nv = 96 ne = 84 npr = 91508 no. pairs analyzed = 91508 no. exposed pairs = 4696 no. arc points = 31363 no. surface atoms = 1598 nbur = 2686 mkacc time = 0.2600000 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= 444 mr = 5507 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.5200000 number of dielectric boundary points 4138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3308 ## 355 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3899477E-09 -3.8182040E-09 midg,1,midg; midg,igrid,midg 7.8640685E-09 -4.0449795E-09 1,midg,midg; igrid,midg,midg -4.4471871E-09 4.6119162E-09 gauss-seidel spectral radius is 0.9849911 estimated iterations to convergence 67 setup time was (sec) 0.8000000 now iterating at: 11:35:09 rms-change max change #iterations 0.1248880 16.08321 at 10iterations 1.0341958E-02 1.399181 at 20iterations 1.0881830E-03 0.1387787 at 30iterations 2.3117260E-04 3.2259017E-02 at 40iterations 7.6077908E-05 1.1351347E-02 at 50iterations finished qdiffx linear iterations at : 11:35:12 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 7.6077908E-05 1.1351347E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 11:35:13 4.395u 0.297s 0:05.15 90.8% 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 11:35:13 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4284 !!! WARNING: HIQ 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.754242 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): -25.46900 35.41200 ymin,ymax (A): 38.07700 97.66900 zmin,zma (A): 30.82600 90.66400 x,y,z range (A): 60.88100 59.59200 59.83800 scale (grids/A): 1.754242 object centre (A): 4.971501 67.87300 60.74500 number of atom coordinates read : 4284 total number of charged atoms : 4126 net assigned charge : -0.9859650 assigned positive charge : 642.9156 centred at (gu) : 91.73760 84.48976 85.31736 assigned negative charge : -643.9046 centred at (gu) : 91.36964 84.94695 85.71881 start vw surface at 0.1900000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 102735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31363 grid for indexing accessible points = 1.400000 m= 36052 mr = 75124 m= 4828 mr = 27401 m= 174 mr = 3013 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6158 time to turn everything in is 0.8800000 number of dielectric boundary points 38216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 32061 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) : 0.5847473 object centre at (A) : 4.971501 67.87300 60.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0221154E-02 -2.7707485E-02 midg,1,midg; midg,igrid,midg 3.7619896E-02 -1.0710406E-02 1,midg,midg; igrid,midg,midg -1.5209288E-02 4.1367516E-02 gauss-seidel spectral radius is 0.9985346 estimated iterations to convergence 207 setup time was (sec) 1.190000 now iterating at: 11:35:14 rms-change max change #iterations 4.798480 169.8482 at 10iterations 2.176158 64.95143 at 20iterations 0.9955181 26.88052 at 30iterations 0.4533980 12.48949 at 40iterations 0.2077604 5.947337 at 50iterations 9.4979309E-02 2.696156 at 60iterations 4.3394282E-02 1.299127 at 70iterations 1.9868784E-02 0.5426483 at 80iterations 9.1224303E-03 0.2693253 at 90iterations 4.1755000E-03 0.1308517 at 100iterations 1.9356087E-03 6.0558319E-02 at 110iterations 9.0778398E-04 2.6931763E-02 at 120iterations finished qdiffx linear iterations at : 11:35:23 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 9.0778398E-04 2.6931763E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.24000 DelPhi exited at 11:35:24 10.241u 0.350s 0:10.93 96.8% 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 11:35:24 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4284 !!! WARNING: HIQ 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.631363 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): -25.46900 35.41200 ymin,ymax (A): 38.07700 97.66900 zmin,zma (A): 30.82600 90.66400 x,y,z range (A): 60.88100 59.59200 59.83800 scale (grids/A): 2.631363 object centre (A): 4.971501 67.87300 60.74500 number of atom coordinates read : 4284 total number of charged atoms : 4126 net assigned charge : -0.9859650 assigned positive charge : 642.9156 centred at (gu) : 92.60613 81.73438 82.97564 assigned negative charge : -643.9046 centred at (gu) : 92.05440 82.42031 83.57804 start vw surface at 0.2000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 238517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31363 grid for indexing accessible points = 1.400000 m= 120747 mr = 181892 m= 40342 mr = 100829 m= 8367 mr = 32880 m= 826 mr = 6329 m= 26 mr = 531 m= 0 mr = 7 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 20887 time to turn everything in is 2.290000 number of dielectric boundary points 86357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.460000 number of grid points assigned charge 32989 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) : 1.754242 object centre at (A) : 4.971501 67.87300 60.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.067101 -0.3217156 midg,1,midg; midg,igrid,midg 0.4832488 -0.1652667 1,midg,midg; igrid,midg,midg -0.2076937 0.4891984 gauss-seidel spectral radius is 0.9992539 estimated iterations to convergence 289 setup time was (sec) 2.650000 now iterating at: 11:35:27 rms-change max change #iterations 11.64257 314.2057 at 10iterations 6.820892 144.9930 at 20iterations 3.952185 68.47958 at 30iterations 2.293856 39.15402 at 40iterations 1.325380 22.45067 at 50iterations 0.7645761 12.57564 at 60iterations 0.4408629 7.213828 at 70iterations 0.2538094 4.685463 at 80iterations 0.1461435 2.200174 at 90iterations 8.4062807E-02 1.331018 at 100iterations 4.8264954E-02 0.8817825 at 110iterations 2.7779637E-02 0.4617548 at 120iterations 1.5998846E-02 0.2626648 at 130iterations 9.2132092E-03 0.1452408 at 140iterations 5.3100022E-03 0.1028061 at 150iterations 3.0794116E-03 5.0476074E-02 at 160iterations 1.7965882E-03 2.8436184E-02 at 170iterations 1.0609161E-03 1.8611431E-02 at 180iterations finished qdiffx linear iterations at : 11:35:42 total time elapsed so far: 17.73000 # loops : 180 mean,max change (kT/e) : 1.0609161E-03 1.8611431E-02 energy calculations done at 17.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.92000 DelPhi exited at 11:35:43 17.921u 0.348s 0:18.81 97.0% 0+0k 0+0io 0pf+0w