Tue Oct 11 07:01:30 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 07:01:30 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 0.5746384 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): 2.207000 60.31300 ymin,ymax (A): -65.91900 -3.967000 zmin,zma (A): -32.51200 17.14500 x,y,z range (A): 58.10600 61.95200 49.65700 scale (grids/A): 0.5746384 object centre (A): 31.26000 -34.94300 -7.683500 number of atom coordinates read : 2960 total number of charged atoms : 2815 net assigned charge : -4.599984 assigned positive charge : 430.5206 centred at (gu) : 89.25212 91.66676 90.64257 assigned negative charge : -435.1211 centred at (gu) : 89.46344 91.56277 90.64275 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6363 nv = 96 ne = 84 npr = 62264 no. pairs analyzed = 62264 no. exposed pairs = 3687 no. arc points = 25868 no. surface atoms = 1252 nbur = 1708 mkacc time = 0.1400000 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 = 1.484000 m= 277 mr = 3368 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2581 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6613726E-10 -1.0365190E-09 midg,1,midg; midg,igrid,midg -1.8807340E-09 1.4526926E-09 1,midg,midg; igrid,midg,midg 3.3722241E-09 -4.0039172E-09 gauss-seidel spectral radius is 0.9843708 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 07:01:31 rms-change max change #iterations 9.2470266E-02 14.04849 at 10iterations 7.1378867E-03 1.189529 at 20iterations 5.3532276E-04 8.2311630E-02 at 30iterations 4.1553554E-05 6.9732666E-03 at 40iterations 3.2790042E-06 4.8255920E-04 at 50iterations finished qdiffx linear iterations at : 07:01:34 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 3.2790042E-06 4.8255920E-04 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 07:01:35 4.192u 0.244s 0:04.80 92.2% 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 07:01:35 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.723915 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): 2.207000 60.31300 ymin,ymax (A): -65.91900 -3.967000 zmin,zma (A): -32.51200 17.14500 x,y,z range (A): 58.10600 61.95200 49.65700 scale (grids/A): 1.723915 object centre (A): 31.26000 -34.94300 -7.683500 number of atom coordinates read : 2960 total number of charged atoms : 2815 net assigned charge : -4.599984 assigned positive charge : 430.5206 centred at (gu) : 87.75578 94.99944 91.92719 assigned negative charge : -435.1211 centred at (gu) : 88.38982 94.68792 91.92805 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25868 grid for indexing accessible points = 1.400000 m= 23186 mr = 47771 m= 2841 mr = 16687 m= 89 mr = 1622 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1637 time to turn everything in is 0.5200000 number of dielectric boundary points 30075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21855 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) : 0.5746384 object centre at (A) : 31.26000 -34.94300 -7.683500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0847811E-03 1.5188404E-02 midg,1,midg; midg,igrid,midg -2.6061373E-02 9.3101561E-03 1,midg,midg; igrid,midg,midg 4.7271005E-03 -3.8299669E-02 gauss-seidel spectral radius is 0.9983755 estimated iterations to convergence 197 setup time was (sec) 0.8500000 now iterating at: 07:01:36 rms-change max change #iterations 3.656394 181.3433 at 10iterations 1.594880 54.33884 at 20iterations 0.6983919 25.96722 at 30iterations 0.3057315 14.71556 at 40iterations 0.1329755 4.667104 at 50iterations 5.8284748E-02 2.077126 at 60iterations 2.5566118E-02 0.8730392 at 70iterations 1.1146871E-02 0.3514614 at 80iterations 4.8795417E-03 0.1823006 at 90iterations 2.1330100E-03 7.2448730E-02 at 100iterations 9.3328534E-04 3.7590027E-02 at 110iterations 4.0901836E-04 1.3057709E-02 at 120iterations finished qdiffx linear iterations at : 07:01:44 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 4.0901836E-04 1.3057709E-02 energy calculations done at 9.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 07:01:45 9.510u 0.292s 0:10.11 96.9% 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 07:01:45 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.585873 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): 2.207000 60.31300 ymin,ymax (A): -65.91900 -3.967000 zmin,zma (A): -32.51200 17.14500 x,y,z range (A): 58.10600 61.95200 49.65700 scale (grids/A): 2.585873 object centre (A): 31.26000 -34.94300 -7.683500 number of atom coordinates read : 2960 total number of charged atoms : 2815 net assigned charge : -4.599984 assigned positive charge : 430.5206 centred at (gu) : 86.63353 97.49905 92.89072 assigned negative charge : -435.1211 centred at (gu) : 87.58461 97.03177 92.89191 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 162309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25868 grid for indexing accessible points = 1.400000 m= 77850 mr = 116558 m= 24910 mr = 62761 m= 4630 mr = 19574 m= 389 mr = 3208 m= 11 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 5511 time to turn everything in is 1.320000 number of dielectric boundary points 67819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 22511 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) : 1.723915 object centre at (A) : 31.26000 -34.94300 -7.683500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7460575E-02 0.2800745 midg,1,midg; midg,igrid,midg -0.2743496 0.2035300 1,midg,midg; igrid,midg,midg 2.1276634E-02 -0.5908627 gauss-seidel spectral radius is 0.9991961 estimated iterations to convergence 278 setup time was (sec) 1.680000 now iterating at: 07:01:47 rms-change max change #iterations 9.100815 289.2286 at 10iterations 5.187372 121.5923 at 20iterations 2.933868 75.27574 at 30iterations 1.657177 39.15217 at 40iterations 0.9357781 20.01414 at 50iterations 0.5259827 10.28252 at 60iterations 0.2962706 6.555793 at 70iterations 0.1666136 3.402826 at 80iterations 9.3765207E-02 1.969663 at 90iterations 5.2527394E-02 1.049922 at 100iterations 2.9479042E-02 0.5608568 at 110iterations 1.6552798E-02 0.3309326 at 120iterations 9.2668850E-03 0.1892204 at 130iterations 5.2027777E-03 0.1097260 at 140iterations 2.9137337E-03 6.0531616E-02 at 150iterations 1.6352080E-03 3.1105042E-02 at 160iterations 9.1619929E-04 1.6288757E-02 at 170iterations 5.1264762E-04 1.1023521E-02 at 180iterations finished qdiffx linear iterations at : 07:02:00 total time elapsed so far: 15.12000 # loops : 180 mean,max change (kT/e) : 5.1264762E-04 1.1023521E-02 energy calculations done at 15.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.30000 DelPhi exited at 07:02:01 15.299u 0.294s 0:16.50 94.4% 0+0k 0+0io 0pf+0w