Sun Oct 9 13:52:12 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 Sun Oct 9 2011 at 13:52:12 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7002912 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): -18.41200 30.73100 ymin,ymax (A): -20.55100 30.28500 zmin,zma (A): 4.184000 48.36000 x,y,z range (A): 49.14300 50.83600 44.17600 scale (grids/A): 0.7002912 object centre (A): 6.159501 4.867000 26.27200 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500021 assigned positive charge : 365.0372 centred at (gu) : 90.52061 90.12478 90.26580 assigned negative charge : -361.5375 centred at (gu) : 90.68015 90.20763 90.34571 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8006 nv = 96 ne = 84 npr = 47631 no. pairs analyzed = 47631 no. exposed pairs = 2994 no. arc points = 20924 no. surface atoms = 1010 nbur = 1365 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4448 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1937 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1013964E-08 -1.4495190E-08 midg,1,midg; midg,igrid,midg 6.4101926E-08 -1.5538511E-08 1,midg,midg; igrid,midg,midg 9.2186575E-08 -5.9550679E-08 gauss-seidel spectral radius is 0.9894069 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 13:52:13 rms-change max change #iterations 0.2124596 28.55331 at 10iterations 2.6135148E-02 3.542968 at 20iterations 3.7895557E-03 0.5143433 at 30iterations 8.8115246E-04 0.1353874 at 40iterations 2.8960212E-04 4.6478271E-02 at 50iterations finished qdiffx linear iterations at : 13:52:15 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.8960212E-04 4.6478271E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 13:52:16 3.099u 0.136s 0:03.55 90.7% 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 Sun Oct 9 2011 at 13:52:16 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 2.100873 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): -18.41200 30.73100 ymin,ymax (A): -20.55100 30.28500 zmin,zma (A): 4.184000 48.36000 x,y,z range (A): 49.14300 50.83600 44.17600 scale (grids/A): 2.100873 object centre (A): 6.159501 4.867000 26.27200 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500021 assigned positive charge : 365.0372 centred at (gu) : 91.56149 90.37394 90.79707 assigned negative charge : -361.5375 centred at (gu) : 92.04015 90.62259 91.03699 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 84832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20924 grid for indexing accessible points = 1.400000 m= 32347 mr = 59179 m= 5712 mr = 24098 m= 481 mr = 3654 m= 12 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.5800000 number of dielectric boundary points 36241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17761 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) : 0.7002912 object centre at (A) : 6.159501 4.867000 26.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2417045E-02 9.4051808E-03 midg,1,midg; midg,igrid,midg -1.5955590E-04 -4.3588646E-02 1,midg,midg; igrid,midg,midg -2.4749013E-03 -4.6252519E-02 gauss-seidel spectral radius is 0.9988500 estimated iterations to convergence 233 setup time was (sec) 0.8400000 now iterating at: 13:52:17 rms-change max change #iterations 5.016750 214.7712 at 10iterations 2.482953 82.97529 at 20iterations 1.236716 35.40331 at 30iterations 0.6171741 19.16857 at 40iterations 0.3079302 8.961706 at 50iterations 0.1539708 4.230652 at 60iterations 7.6890506E-02 2.147807 at 70iterations 3.8589653E-02 1.066801 at 80iterations 1.9406920E-02 0.5617476 at 90iterations 9.8860245E-03 0.2755394 at 100iterations 5.1204530E-03 0.1452560 at 110iterations 2.7508684E-03 8.2183838E-02 at 120iterations finished qdiffx linear iterations at : 13:52:23 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 2.7508684E-03 8.2183838E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 13:52:23 7.025u 0.166s 0:07.51 95.6% 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 Sun Oct 9 2011 at 13:52:23 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.151310 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): -18.41200 30.73100 ymin,ymax (A): -20.55100 30.28500 zmin,zma (A): 4.184000 48.36000 x,y,z range (A): 49.14300 50.83600 44.17600 scale (grids/A): 3.151310 object centre (A): 6.159501 4.867000 26.27200 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500021 assigned positive charge : 365.0372 centred at (gu) : 92.34214 90.56087 91.19539 assigned negative charge : -361.5375 centred at (gu) : 93.06025 90.93385 91.55548 start vw surface at 0.1300000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 195729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20924 grid for indexing accessible points = 1.400000 m= 102757 mr = 142851 m= 39309 mr = 84698 m= 10538 mr = 31778 m= 1970 mr = 8019 m= 178 mr = 1411 m= 7 mr = 97 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1039 time to turn everything in is 1.840000 number of dielectric boundary points 81632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 17872 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) : 2.100873 object centre at (A) : 6.159501 4.867000 26.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5809572 -8.0422889E-03 midg,1,midg; midg,igrid,midg -0.3231035 -0.6764621 1,midg,midg; igrid,midg,midg -0.1034713 -0.6444961 gauss-seidel spectral radius is 0.9993074 estimated iterations to convergence 300 setup time was (sec) 2.120000 now iterating at: 13:52:26 rms-change max change #iterations 11.25841 409.8920 at 10iterations 6.721752 136.8819 at 20iterations 3.993139 78.70587 at 30iterations 2.369364 40.60824 at 40iterations 1.402480 25.67615 at 50iterations 0.8276426 14.80682 at 60iterations 0.4889783 8.754930 at 70iterations 0.2876688 5.029448 at 80iterations 0.1694324 2.746105 at 90iterations 9.9986233E-02 1.636355 at 100iterations 5.8963969E-02 0.9653549 at 110iterations 3.5095520E-02 0.5868120 at 120iterations 2.0975003E-02 0.3766479 at 130iterations 1.2776119E-02 0.2189789 at 140iterations 8.0510853E-03 0.1567993 at 150iterations 5.3201197E-03 0.1068192 at 160iterations 3.7364750E-03 7.6873779E-02 at 170iterations 2.7927081E-03 5.6461334E-02 at 180iterations finished qdiffx linear iterations at : 13:52:35 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 2.7927081E-03 5.6461334E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 13:52:36 11.959u 0.185s 0:12.49 97.1% 0+0k 0+0io 0pf+0w