Sat Oct 8 15:07:21 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 15:07:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3132 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: 0.5998618 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): 2.365000 61.71200 ymin,ymax (A): -21.66200 26.59000 zmin,zma (A): -9.379000 45.28300 x,y,z range (A): 59.34700 48.25200 54.66200 scale (grids/A): 0.5998618 object centre (A): 32.03850 2.464001 17.95200 number of atom coordinates read : 3132 total number of charged atoms : 2989 net assigned charge : 2.000009 assigned positive charge : 465.8291 centred at (gu) : 90.09841 89.24283 90.89981 assigned negative charge : -463.8301 centred at (gu) : 90.08772 89.20273 90.93311 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7429 nv = 96 ne = 84 npr = 64398 no. pairs analyzed = 64398 no. exposed pairs = 3672 no. arc points = 26213 no. surface atoms = 1233 nbur = 1899 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 4205 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2647 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8936579E-09 -7.1284878E-10 midg,1,midg; midg,igrid,midg -1.0423098E-09 2.2008757E-09 1,midg,midg; igrid,midg,midg 4.0827844E-10 1.3745656E-09 gauss-seidel spectral radius is 0.9856589 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 15:07:22 rms-change max change #iterations 0.1200917 15.76947 at 10iterations 1.0917255E-02 1.494551 at 20iterations 1.0600118E-03 0.1528549 at 30iterations 1.2676379E-04 1.8632889E-02 at 40iterations 2.0038055E-05 3.0517578E-03 at 50iterations finished qdiffx linear iterations at : 15:07:25 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.0038055E-05 3.0517578E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:07:25 3.552u 0.198s 0:04.09 91.4% 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 Sat Oct 8 2011 at 15:07:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3132 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: 1.799585 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): 2.365000 61.71200 ymin,ymax (A): -21.66200 26.59000 zmin,zma (A): -9.379000 45.28300 x,y,z range (A): 59.34700 48.25200 54.66200 scale (grids/A): 1.799585 object centre (A): 32.03850 2.464001 17.95200 number of atom coordinates read : 3132 total number of charged atoms : 2989 net assigned charge : 2.000009 assigned positive charge : 465.8291 centred at (gu) : 90.29449 87.72749 92.69882 assigned negative charge : -463.8301 centred at (gu) : 90.26303 87.60783 92.79924 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26213 grid for indexing accessible points = 1.400000 m= 27914 mr = 58572 m= 3497 mr = 20336 m= 146 mr = 2023 m= 0 mr = 48 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 717 time to turn everything in is 0.3900000 number of dielectric boundary points 32900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23335 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) : 0.5998618 object centre at (A) : 32.03850 2.464001 17.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0114824E-02 -1.7648980E-02 midg,1,midg; midg,igrid,midg -2.2135077E-03 7.2763865E-03 1,midg,midg; igrid,midg,midg 2.8917849E-02 1.0201370E-02 gauss-seidel spectral radius is 0.9985276 estimated iterations to convergence 207 setup time was (sec) 0.6200000 now iterating at: 15:07:26 rms-change max change #iterations 4.170878 182.0608 at 10iterations 1.887669 60.27539 at 20iterations 0.8594167 32.75663 at 30iterations 0.3919477 13.33389 at 40iterations 0.1786404 5.610779 at 50iterations 8.1151798E-02 2.786193 at 60iterations 3.7081480E-02 1.300240 at 70iterations 1.6891630E-02 0.5392952 at 80iterations 7.7241170E-03 0.2636118 at 90iterations 3.5237963E-03 0.1126995 at 100iterations 1.6027323E-03 4.8904419E-02 at 110iterations 7.3194189E-04 2.4353027E-02 at 120iterations finished qdiffx linear iterations at : 15:07:34 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 7.3194189E-04 2.4353027E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 15:07:34 8.161u 0.221s 0:08.67 96.6% 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 15:07:34 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3132 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: 2.699378 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): 2.365000 61.71200 ymin,ymax (A): -21.66200 26.59000 zmin,zma (A): -9.379000 45.28300 x,y,z range (A): 59.34700 48.25200 54.66200 scale (grids/A): 2.699378 object centre (A): 32.03850 2.464001 17.95200 number of atom coordinates read : 3132 total number of charged atoms : 2989 net assigned charge : 2.000009 assigned positive charge : 465.8291 centred at (gu) : 90.44140 86.59100 94.04817 assigned negative charge : -463.8301 centred at (gu) : 90.39449 86.41154 94.19882 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 191241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26213 grid for indexing accessible points = 1.400000 m= 94079 mr = 142363 m= 30007 mr = 76955 m= 5722 mr = 23570 m= 605 mr = 4092 m= 31 mr = 366 m= 0 mr = 15 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 2302 time to turn everything in is 1.010000 number of dielectric boundary points 74324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 23907 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) : 1.799585 object centre at (A) : 32.03850 2.464001 17.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1246147 -0.2078378 midg,1,midg; midg,igrid,midg -3.2200612E-02 0.1144083 1,midg,midg; igrid,midg,midg 0.4788735 0.1960702 gauss-seidel spectral radius is 0.9992358 estimated iterations to convergence 286 setup time was (sec) 1.270000 now iterating at: 15:07:36 rms-change max change #iterations 9.924135 417.7621 at 10iterations 5.721420 138.5547 at 20iterations 3.284537 78.86517 at 30iterations 1.880457 33.68972 at 40iterations 1.075246 19.20741 at 50iterations 0.6138158 11.04656 at 60iterations 0.3503299 6.387205 at 70iterations 0.1999512 3.620716 at 80iterations 0.1138452 2.075130 at 90iterations 6.4780720E-02 1.154319 at 100iterations 3.6938999E-02 0.6621437 at 110iterations 2.1027969E-02 0.3814392 at 120iterations 1.2013443E-02 0.2566967 at 130iterations 6.8508391E-03 0.1213455 at 140iterations 3.9140759E-03 7.0135117E-02 at 150iterations 2.2450432E-03 3.8124084E-02 at 160iterations 1.2873888E-03 2.2183180E-02 at 170iterations 7.4205775E-04 1.3004303E-02 at 180iterations finished qdiffx linear iterations at : 15:07:48 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 7.4205775E-04 1.3004303E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 15:07:48 13.283u 0.224s 0:13.77 98.0% 0+0k 0+0io 0pf+0w