Sat Oct 15 13:45:01 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+sph.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 = amb.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 15 2011 at 13:45:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 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: 0.6113687 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): -27.74800 25.51700 ymin,ymax (A): -25.87900 32.35100 zmin,zma (A): -29.66400 17.96700 x,y,z range (A): 53.26500 58.23000 47.63100 scale (grids/A): 0.6113687 object centre (A): -1.115499 3.236001 -5.848500 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : -2.999975 assigned positive charge : 451.0871 centred at (gu) : 90.13788 89.03326 90.69148 assigned negative charge : -454.0879 centred at (gu) : 90.05721 88.91371 90.53171 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7212 nv = 96 ne = 84 npr = 58466 no. pairs analyzed = 58466 no. exposed pairs = 3572 no. arc points = 25683 no. surface atoms = 1194 nbur = 1723 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3988 m= 0 mr = 44 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3500000 number of dielectric boundary points 3562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2564 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9655253E-09 8.9407939E-09 midg,1,midg; midg,igrid,midg -1.1376965E-08 4.2212944E-09 1,midg,midg; igrid,midg,midg -6.5369750E-09 3.0801584E-09 gauss-seidel spectral radius is 0.9861745 estimated iterations to convergence 70 setup time was (sec) 0.6900000 now iterating at: 13:45:02 rms-change max change #iterations 0.1274304 19.80758 at 10iterations 1.1570008E-02 1.728722 at 20iterations 1.0746075E-03 0.1582088 at 30iterations 1.4295201E-04 2.6193619E-02 at 40iterations 3.8363443E-05 7.8754425E-03 at 50iterations finished qdiffx linear iterations at : 13:45:07 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 3.8363443E-05 7.8754425E-03 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.330000 DelPhi exited at 13:45:07 5.334u 0.438s 0:06.07 94.8% 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 Sat Oct 15 2011 at 13:45:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 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: 1.834106 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): -27.74800 25.51700 ymin,ymax (A): -25.87900 32.35100 zmin,zma (A): -29.66400 17.96700 x,y,z range (A): 53.26500 58.23000 47.63100 scale (grids/A): 1.834106 object centre (A): -1.115499 3.236001 -5.848500 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : -2.999975 assigned positive charge : 451.0871 centred at (gu) : 90.41259 87.09921 92.07397 assigned negative charge : -454.0879 centred at (gu) : 90.17113 86.74093 91.59464 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25683 grid for indexing accessible points = 1.400000 m= 27751 mr = 55167 m= 4089 mr = 20246 m= 191 mr = 2472 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1185 time to turn everything in is 0.6700000 number of dielectric boundary points 32928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 21645 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) : 0.6113687 object centre at (A) : -1.115499 3.236001 -5.848500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0994079E-02 7.8840517E-03 midg,1,midg; midg,igrid,midg -5.7697389E-02 2.3175035E-02 1,midg,midg; igrid,midg,midg 2.5177118E-03 -2.8359303E-03 gauss-seidel spectral radius is 0.9985617 estimated iterations to convergence 209 setup time was (sec) 1.030000 now iterating at: 13:45:09 rms-change max change #iterations 4.292418 176.7582 at 10iterations 1.957540 63.92772 at 20iterations 0.9057427 27.84873 at 30iterations 0.4152121 14.58216 at 40iterations 0.1914885 5.815533 at 50iterations 8.8004723E-02 2.659728 at 60iterations 4.0375128E-02 1.273439 at 70iterations 1.8545058E-02 0.5302944 at 80iterations 8.5154604E-03 0.2785559 at 90iterations 3.9363033E-03 0.1193962 at 100iterations 1.8293249E-03 5.4221153E-02 at 110iterations 8.5846178E-04 2.5500298E-02 at 120iterations finished qdiffx linear iterations at : 13:45:21 total time elapsed so far: 12.92000 # loops : 120 mean,max change (kT/e) : 8.5846178E-04 2.5500298E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 13:45:21 13.093u 0.509s 0:13.89 97.8% 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 Sat Oct 15 2011 at 13:45:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 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: 2.751159 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): -27.74800 25.51700 ymin,ymax (A): -25.87900 32.35100 zmin,zma (A): -29.66400 17.96700 x,y,z range (A): 53.26500 58.23000 47.63100 scale (grids/A): 2.751159 object centre (A): -1.115499 3.236001 -5.848500 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : -2.999975 assigned positive charge : 451.0871 centred at (gu) : 90.61884 85.64863 93.11075 assigned negative charge : -454.0879 centred at (gu) : 90.25658 85.11124 92.39177 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 182393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25683 grid for indexing accessible points = 1.400000 m= 90521 mr = 133302 m= 31868 mr = 73940 m= 7112 mr = 25388 m= 847 mr = 5263 m= 53 mr = 534 m= 0 mr = 23 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 3872 time to turn everything in is 1.720000 number of dielectric boundary points 74344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 22140 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) : 1.834106 object centre at (A) : -1.115499 3.236001 -5.848500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7146523E-02 -1.3795587E-02 midg,1,midg; midg,igrid,midg -0.9497778 0.3578875 1,midg,midg; igrid,midg,midg 7.0667826E-02 -7.9695351E-02 gauss-seidel spectral radius is 0.9992456 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 13:45:24 rms-change max change #iterations 10.27524 379.3431 at 10iterations 6.020999 136.1019 at 20iterations 3.506239 65.18627 at 30iterations 2.031028 45.35690 at 40iterations 1.171381 25.55070 at 50iterations 0.6758980 13.06046 at 60iterations 0.3883181 7.487717 at 70iterations 0.2231694 4.866437 at 80iterations 0.1281309 2.451388 at 90iterations 7.3418744E-02 1.441372 at 100iterations 4.2088579E-02 0.8317032 at 110iterations 2.4106547E-02 0.4863840 at 120iterations 1.3820507E-02 0.2393255 at 130iterations 7.9086386E-03 0.1382757 at 140iterations 4.5318617E-03 8.3248138E-02 at 150iterations 2.5924984E-03 4.7159195E-02 at 160iterations 1.4865500E-03 3.3168793E-02 at 170iterations 8.5322961E-04 1.4244080E-02 at 180iterations finished qdiffx linear iterations at : 13:45:43 total time elapsed so far: 21.22000 # loops : 180 mean,max change (kT/e) : 8.5322961E-04 1.4244080E-02 energy calculations done at 21.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.38000 DelPhi exited at 13:45:44 21.382u 0.561s 0:22.25 98.6% 0+0k 0+0io 0pf+0w