Wed Dec 28 11:02:43 PST 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 Wed Dec 28 2011 at 11:02:43 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6437497 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): -5.357000 34.68300 ymin,ymax (A): -3.396000 49.37400 zmin,zma (A): -24.42700 30.87400 x,y,z range (A): 40.04000 52.77000 55.30100 scale (grids/A): 0.6437497 object centre (A): 14.66300 22.98900 3.223500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 90.70016 92.29945 90.26767 assigned negative charge : -289.4262 centred at (gu) : 90.81390 92.45588 90.21086 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5610 nv = 96 ne = 84 npr = 40249 no. pairs analyzed = 40249 no. exposed pairs = 2460 no. arc points = 17319 no. surface atoms = 832 nbur = 1132 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 3144 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2600000 number of dielectric boundary points 2715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6560456E-09 9.6279740E-09 midg,1,midg; midg,igrid,midg 1.1302019E-08 -1.9262229E-08 1,midg,midg; igrid,midg,midg 1.2431338E-08 -8.5460545E-09 gauss-seidel spectral radius is 0.9874406 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 11:02:44 rms-change max change #iterations 0.1292865 19.81827 at 10iterations 1.2910543E-02 2.128761 at 20iterations 1.2828526E-03 0.2092972 at 30iterations 1.2864203E-04 1.9986153E-02 at 40iterations 1.2832853E-05 2.0766258E-03 at 50iterations finished qdiffx linear iterations at : 11:02:48 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.2832853E-05 2.0766258E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 11:02:49 4.787u 0.388s 0:05.93 87.0% 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 Wed Dec 28 2011 at 11:02:49 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.931249 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): -5.357000 34.68300 ymin,ymax (A): -3.396000 49.37400 zmin,zma (A): -24.42700 30.87400 x,y,z range (A): 40.04000 52.77000 55.30100 scale (grids/A): 1.931249 object centre (A): 14.66300 22.98900 3.223500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 92.10053 96.89857 90.80293 assigned negative charge : -289.4262 centred at (gu) : 92.44170 97.36783 90.63268 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17319 grid for indexing accessible points = 1.400000 m= 22539 mr = 41431 m= 3620 mr = 17229 m= 204 mr = 2485 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1410 time to turn everything in is 0.5100000 number of dielectric boundary points 24964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14464 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) : 0.6437497 object centre at (A) : 14.66300 22.98900 3.223500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1616965E-02 7.5085964E-03 midg,1,midg; midg,igrid,midg 3.3968881E-02 -1.7751046E-02 1,midg,midg; igrid,midg,midg 7.7979034E-03 -5.1439856E-03 gauss-seidel spectral radius is 0.9985940 estimated iterations to convergence 211 setup time was (sec) 0.8000000 now iterating at: 11:02:50 rms-change max change #iterations 3.706592 159.6255 at 10iterations 1.717096 64.85436 at 20iterations 0.7973878 27.31215 at 30iterations 0.3688444 14.64314 at 40iterations 0.1706596 6.003385 at 50iterations 7.8668326E-02 2.783215 at 60iterations 3.6528517E-02 1.370691 at 70iterations 1.6885730E-02 0.6400089 at 80iterations 7.8352671E-03 0.2629585 at 90iterations 3.6235608E-03 0.1373138 at 100iterations 1.6815558E-03 5.5774808E-02 at 110iterations 7.7959400E-04 2.8042555E-02 at 120iterations finished qdiffx linear iterations at : 11:03:00 total time elapsed so far: 10.93000 # loops : 120 mean,max change (kT/e) : 7.7959400E-04 2.8042555E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 11:03:02 11.105u 0.449s 0:12.57 91.8% 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 Wed Dec 28 2011 at 11:03:02 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.896873 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): -5.357000 34.68300 ymin,ymax (A): -3.396000 49.37400 zmin,zma (A): -24.42700 30.87400 x,y,z range (A): 40.04000 52.77000 55.30100 scale (grids/A): 2.896873 object centre (A): 14.66300 22.98900 3.223500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 291.4260 centred at (gu) : 93.15066 100.3480 91.20451 assigned negative charge : -289.4262 centred at (gu) : 93.66261 101.0517 90.94901 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 138110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17319 grid for indexing accessible points = 1.400000 m= 71688 mr = 99861 m= 27129 mr = 59703 m= 6640 mr = 22753 m= 936 mr = 5325 m= 54 mr = 649 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 4571 time to turn everything in is 1.300000 number of dielectric boundary points 56236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 14656 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) : 1.931249 object centre at (A) : 14.66300 22.98900 3.223500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9944758 -1.3129598E-02 midg,1,midg; midg,igrid,midg 0.3358904 -0.1898836 1,midg,midg; igrid,midg,midg 4.2625580E-02 -3.4850288E-02 gauss-seidel spectral radius is 0.9992344 estimated iterations to convergence 285 setup time was (sec) 1.640000 now iterating at: 11:03:04 rms-change max change #iterations 8.703874 375.8544 at 10iterations 5.000005 111.9369 at 20iterations 2.846004 61.68240 at 30iterations 1.619596 34.53974 at 40iterations 0.9217670 19.47832 at 50iterations 0.5238340 10.77985 at 60iterations 0.2982077 5.846548 at 70iterations 0.1690581 3.661776 at 80iterations 9.5878437E-02 1.982383 at 90iterations 5.4258976E-02 1.135195 at 100iterations 3.0887390E-02 0.6072731 at 110iterations 1.7548710E-02 0.3386545 at 120iterations 9.9340212E-03 0.2018509 at 130iterations 5.6547462E-03 0.1096115 at 140iterations 3.2081425E-03 6.4041138E-02 at 150iterations 1.8231722E-03 3.4778595E-02 at 160iterations 1.0365623E-03 2.2550583E-02 at 170iterations 5.8915344E-04 1.1414528E-02 at 180iterations finished qdiffx linear iterations at : 11:03:19 total time elapsed so far: 17.28000 # loops : 180 mean,max change (kT/e) : 5.8915344E-04 1.1414528E-02 energy calculations done at 17.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.45000 DelPhi exited at 11:03:20 17.453u 0.461s 0:18.56 96.4% 0+0k 0+0io 0pf+0w