Tue Nov 22 14:12:13 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 Tue Nov 22 2011 at 14:12:18 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5681546 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): -34.50900 12.48700 ymin,ymax (A): 0.3390000 41.60500 zmin,zma (A): -1.467000 61.19200 x,y,z range (A): 46.99600 41.26600 62.65900 scale (grids/A): 0.5681546 object centre (A): -11.01100 20.97200 29.86250 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 288.5840 centred at (gu) : 89.59547 89.71004 88.83228 assigned negative charge : -283.5844 centred at (gu) : 89.49249 89.86355 88.81301 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4244 nv = 96 ne = 84 npr = 39565 no. pairs analyzed = 39565 no. exposed pairs = 2442 no. arc points = 17469 no. surface atoms = 829 nbur = 1119 mkacc time = 9.0000004E-02 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 = 1.540000 m= 200 mr = 2250 m= 0 mr = 22 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1827 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0412060E-10 6.8718647E-10 midg,1,midg; midg,igrid,midg 2.2894839E-09 -6.9571632E-10 1,midg,midg; igrid,midg,midg -2.8999952E-10 1.5225929E-09 gauss-seidel spectral radius is 0.9839341 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 14:12:22 rms-change max change #iterations 7.3203094E-02 12.96032 at 10iterations 5.4769656E-03 0.8882580 at 20iterations 3.9071520E-04 7.6756477E-02 at 30iterations 2.8844255E-05 4.8942566E-03 at 40iterations 2.1574224E-06 4.4250488E-04 at 50iterations finished qdiffx linear iterations at : 14:12:30 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 2.1574224E-06 4.4250488E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:12:32 3.199u 0.142s 0:14.60 22.8% 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 Tue Nov 22 2011 at 14:12:37 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.704464 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): -34.50900 12.48700 ymin,ymax (A): 0.3390000 41.60500 zmin,zma (A): -1.467000 61.19200 x,y,z range (A): 46.99600 41.26600 62.65900 scale (grids/A): 1.704464 object centre (A): -11.01100 20.97200 29.86250 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 288.5840 centred at (gu) : 88.78655 89.13036 86.49710 assigned negative charge : -283.5844 centred at (gu) : 88.47771 89.59084 86.43929 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 46250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17469 grid for indexing accessible points = 1.400000 m= 15852 mr = 31236 m= 2006 mr = 11668 m= 84 mr = 1181 m= 0 mr = 26 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.3400000 number of dielectric boundary points 20081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14061 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) : 0.5681546 object centre at (A) : -11.01100 20.97200 29.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1645447E-02 1.6414871E-02 midg,1,midg; midg,igrid,midg 8.4242355E-03 -4.8536337E-03 1,midg,midg; igrid,midg,midg -6.8915676E-04 1.5483883E-03 gauss-seidel spectral radius is 0.9982185 estimated iterations to convergence 188 setup time was (sec) 0.6000000 now iterating at: 14:12:42 rms-change max change #iterations 2.886926 159.8133 at 10iterations 1.208147 57.54288 at 20iterations 0.5080165 22.58094 at 30iterations 0.2132904 9.536524 at 40iterations 8.9439414E-02 4.190521 at 50iterations 3.7522007E-02 1.491295 at 60iterations 1.5750896E-02 0.6795959 at 70iterations 6.6502891E-03 0.2618942 at 80iterations 2.7868669E-03 0.1084881 at 90iterations 1.1720551E-03 4.7760010E-02 at 100iterations 4.9198116E-04 1.8413544E-02 at 110iterations 2.0699154E-04 8.4953308E-03 at 120iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 2.0699154E-04 8.4953308E-03 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 14:13:03 6.823u 0.185s 0:26.82 26.0% 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 Tue Nov 22 2011 at 14:13:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.556696 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): -34.50900 12.48700 ymin,ymax (A): 0.3390000 41.60500 zmin,zma (A): -1.467000 61.19200 x,y,z range (A): 46.99600 41.26600 62.65900 scale (grids/A): 2.556696 object centre (A): -11.01100 20.97200 29.86250 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 288.5840 centred at (gu) : 88.17982 88.69537 84.74554 assigned negative charge : -283.5844 centred at (gu) : 87.71662 89.38633 84.65898 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 106853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17469 grid for indexing accessible points = 1.400000 m= 52575 mr = 75899 m= 17561 mr = 42885 m= 3542 mr = 14085 m= 425 mr = 2611 m= 13 mr = 272 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 627 time to turn everything in is 0.7900000 number of dielectric boundary points 45217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 14540 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) : 1.704464 object centre at (A) : -11.01100 20.97200 29.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2323813 0.1511527 midg,1,midg; midg,igrid,midg 7.8874148E-02 -7.5340055E-02 1,midg,midg; igrid,midg,midg -2.3413897E-02 2.4539886E-02 gauss-seidel spectral radius is 0.9991134 estimated iterations to convergence 265 setup time was (sec) 1.070000 now iterating at: 14:13:12 rms-change max change #iterations 7.133457 267.0612 at 10iterations 3.932757 112.1548 at 20iterations 2.150834 57.09085 at 30iterations 1.173655 30.46321 at 40iterations 0.6374263 15.13858 at 50iterations 0.3484422 8.963985 at 60iterations 0.1895246 5.028064 at 70iterations 0.1028959 2.519161 at 80iterations 5.6027889E-02 1.759193 at 90iterations 3.0454177E-02 0.6979256 at 100iterations 1.6566047E-02 0.3677025 at 110iterations 9.0352520E-03 0.2058773 at 120iterations 4.9100243E-03 0.1157122 at 130iterations 2.6567634E-03 6.4041138E-02 at 140iterations 1.4470771E-03 3.2238007E-02 at 150iterations 7.8708783E-04 1.8415689E-02 at 160iterations 4.2745617E-04 9.2666149E-03 at 170iterations 2.3225023E-04 5.5335760E-03 at 180iterations finished qdiffx linear iterations at : 14:13:40 total time elapsed so far: 10.33000 # loops : 180 mean,max change (kT/e) : 2.3225023E-04 5.5335760E-03 energy calculations done at 10.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 14:13:42 10.501u 0.190s 0:37.86 28.2% 0+0k 0+0io 0pf+0w