Tue Oct 11 08:07:08 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 Tue Oct 11 2011 at 08:07:08 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5649628 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): -19.09200 25.42200 ymin,ymax (A): 17.01000 80.02300 zmin,zma (A): 2.263000 51.62300 x,y,z range (A): 44.51400 63.01300 49.36000 scale (grids/A): 0.5649628 object centre (A): 3.165000 48.51650 26.94300 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 7.000014 assigned positive charge : 362.1552 centred at (gu) : 90.04021 88.60948 91.59402 assigned negative charge : -355.1559 centred at (gu) : 89.91838 88.67370 91.55377 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4965 nv = 96 ne = 84 npr = 48023 no. pairs analyzed = 48023 no. exposed pairs = 3198 no. arc points = 22632 no. surface atoms = 1072 nbur = 1320 mkacc time = 0.1400000 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= 221 mr = 2426 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3600000 number of dielectric boundary points 2748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1580405E-10 1.8899871E-09 midg,1,midg; midg,igrid,midg 2.1493811E-09 1.4823506E-10 1,midg,midg; igrid,midg,midg -4.2087356E-10 2.1525410E-09 gauss-seidel spectral radius is 0.9837912 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 08:07:09 rms-change max change #iterations 7.5135939E-02 14.69860 at 10iterations 5.8223647E-03 1.006547 at 20iterations 7.0767925E-04 0.1707001 at 30iterations 1.8126589E-04 4.8812866E-02 at 40iterations 5.4982040E-05 1.4881134E-02 at 50iterations finished qdiffx linear iterations at : 08:07:12 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 5.4982040E-05 1.4881134E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 08:07:13 4.138u 0.214s 0:04.79 90.6% 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 Tue Oct 11 2011 at 08:07:13 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.694888 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): -19.09200 25.42200 ymin,ymax (A): 17.01000 80.02300 zmin,zma (A): 2.263000 51.62300 x,y,z range (A): 44.51400 63.01300 49.36000 scale (grids/A): 1.694888 object centre (A): 3.165000 48.51650 26.94300 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 7.000014 assigned positive charge : 362.1552 centred at (gu) : 90.12016 85.82822 94.78152 assigned negative charge : -355.1559 centred at (gu) : 89.75499 86.02104 94.66103 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 54858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22632 grid for indexing accessible points = 1.400000 m= 16698 mr = 36013 m= 1881 mr = 11195 m= 64 mr = 914 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 25374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17379 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) : 0.5649628 object centre at (A) : 3.165000 48.51650 26.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1260415E-03 1.3678509E-02 midg,1,midg; midg,igrid,midg 4.1595936E-02 2.4022438E-02 1,midg,midg; igrid,midg,midg -6.8688891E-03 1.0796130E-02 gauss-seidel spectral radius is 0.9982550 estimated iterations to convergence 190 setup time was (sec) 0.8800000 now iterating at: 08:07:14 rms-change max change #iterations 3.208313 171.9341 at 10iterations 1.349016 53.65933 at 20iterations 0.5704622 23.04907 at 30iterations 0.2411608 8.921405 at 40iterations 0.1020779 3.746968 at 50iterations 4.3345023E-02 1.626888 at 60iterations 1.8483788E-02 0.6695538 at 70iterations 7.9461057E-03 0.2997208 at 80iterations 3.4903744E-03 0.1591339 at 90iterations 1.6081018E-03 6.7447662E-02 at 100iterations 8.0645754E-04 4.1766167E-02 at 110iterations 4.5647792E-04 2.6058197E-02 at 120iterations finished qdiffx linear iterations at : 08:07:21 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 4.5647792E-04 2.6058197E-02 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.680000 DelPhi exited at 08:07:22 8.679u 0.181s 0:09.44 93.7% 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 Tue Oct 11 2011 at 08:07:22 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 2.542332 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): -19.09200 25.42200 ymin,ymax (A): 17.01000 80.02300 zmin,zma (A): 2.263000 51.62300 x,y,z range (A): 44.51400 63.01300 49.36000 scale (grids/A): 2.542332 object centre (A): 3.165000 48.51650 26.94300 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 7.000014 assigned positive charge : 362.1552 centred at (gu) : 90.18006 83.74232 97.17226 assigned negative charge : -355.1559 centred at (gu) : 89.63248 84.03152 96.99142 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 127374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22632 grid for indexing accessible points = 1.400000 m= 57059 mr = 88648 m= 16652 mr = 44272 m= 2896 mr = 12135 m= 253 mr = 1857 m= 6 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 57205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18022 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) : 1.694888 object centre at (A) : 3.165000 48.51650 26.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4645145E-03 0.1838492 midg,1,midg; midg,igrid,midg 0.6125259 0.3874331 1,midg,midg; igrid,midg,midg -9.2285670E-02 0.1400694 gauss-seidel spectral radius is 0.9991481 estimated iterations to convergence 271 setup time was (sec) 1.570000 now iterating at: 08:07:24 rms-change max change #iterations 8.223345 329.8688 at 10iterations 4.636990 123.7817 at 20iterations 2.600209 69.64388 at 30iterations 1.454418 40.09836 at 40iterations 0.8122874 21.38249 at 50iterations 0.4511677 11.50107 at 60iterations 0.2504205 5.947903 at 70iterations 0.1389961 3.001736 at 80iterations 7.6893918E-02 2.045675 at 90iterations 4.2643666E-02 1.117363 at 100iterations 2.3541255E-02 0.5495338 at 110iterations 1.3081592E-02 0.2905493 at 120iterations 7.2970297E-03 0.1802444 at 130iterations 4.0966221E-03 0.1134472 at 140iterations 2.3410285E-03 5.8900833E-02 at 150iterations 1.3836402E-03 3.9802551E-02 at 160iterations 8.5385476E-04 2.4311066E-02 at 170iterations 5.6505413E-04 1.6979218E-02 at 180iterations finished qdiffx linear iterations at : 08:07:36 total time elapsed so far: 13.47000 # loops : 180 mean,max change (kT/e) : 5.6505413E-04 1.6979218E-02 energy calculations done at 13.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 08:07:36 13.724u 0.176s 0:14.21 97.7% 0+0k 0+0io 0pf+0w