Mon Oct 10 19:31:56 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 Mon Oct 10 2011 at 19:31:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 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: 0.6075085 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): -34.13300 21.60100 ymin,ymax (A): 39.28800 88.28400 zmin,zma (A): 0.1240000 58.72400 x,y,z range (A): 55.73400 48.99599 58.60000 scale (grids/A): 0.6075085 object centre (A): -6.266002 63.78600 29.42400 number of atom coordinates read : 2899 total number of charged atoms : 2757 net assigned charge : 0.5000129 assigned positive charge : 439.5302 centred at (gu) : 92.23209 89.64289 88.85497 assigned negative charge : -439.0310 centred at (gu) : 92.17123 89.62096 88.87413 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7009 nv = 96 ne = 84 npr = 59117 no. pairs analyzed = 59117 no. exposed pairs = 3738 no. arc points = 25578 no. surface atoms = 1273 nbur = 1626 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3696 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2535 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5195906E-09 -6.1863042E-10 midg,1,midg; midg,igrid,midg -1.0312098E-09 1.2112971E-09 1,midg,midg; igrid,midg,midg -1.7944908E-09 5.5287166E-09 gauss-seidel spectral radius is 0.9859994 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 19:31:57 rms-change max change #iterations 0.1199255 17.70549 at 10iterations 1.0481532E-02 1.615458 at 20iterations 9.4681134E-04 0.1327705 at 30iterations 1.0240363E-04 1.5762329E-02 at 40iterations 1.7096732E-05 2.5863647E-03 at 50iterations finished qdiffx linear iterations at : 19:32:00 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.7096732E-05 2.5863647E-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) 3.640000 DelPhi exited at 19:32:00 3.642u 0.210s 0:04.46 86.3% 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 Mon Oct 10 2011 at 19:32:01 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 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: 1.822526 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): -34.13300 21.60100 ymin,ymax (A): 39.28800 88.28400 zmin,zma (A): 0.1240000 58.72400 x,y,z range (A): 55.73400 48.99599 58.60000 scale (grids/A): 1.822526 object centre (A): -6.266002 63.78600 29.42400 number of atom coordinates read : 2899 total number of charged atoms : 2757 net assigned charge : 0.5000129 assigned positive charge : 439.5302 centred at (gu) : 96.69553 88.92769 86.56406 assigned negative charge : -439.0310 centred at (gu) : 96.51326 88.86225 86.62189 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 76292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25578 grid for indexing accessible points = 1.400000 m= 25569 mr = 52052 m= 3321 mr = 18000 m= 136 mr = 1758 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 33500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21596 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) : 0.6075085 object centre at (A) : -6.266002 63.78600 29.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3169437E-03 -5.3835504E-02 midg,1,midg; midg,igrid,midg 1.5996308E-03 8.5546598E-03 1,midg,midg; igrid,midg,midg -8.7687438E-03 8.2867779E-03 gauss-seidel spectral radius is 0.9985390 estimated iterations to convergence 207 setup time was (sec) 0.9400000 now iterating at: 19:32:02 rms-change max change #iterations 4.206910 168.4009 at 10iterations 1.921332 63.63245 at 20iterations 0.8771100 29.17232 at 30iterations 0.3995984 14.05960 at 40iterations 0.1827087 6.441696 at 50iterations 8.3334722E-02 2.714410 at 60iterations 3.8000230E-02 1.194700 at 70iterations 1.7332673E-02 0.5603790 at 80iterations 7.9164058E-03 0.2638483 at 90iterations 3.6069683E-03 0.1437874 at 100iterations 1.6564445E-03 5.3789139E-02 at 110iterations 7.5537426E-04 2.4721384E-02 at 120iterations finished qdiffx linear iterations at : 19:32:08 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 7.5537426E-04 2.4721384E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 19:32:09 7.712u 0.208s 0:08.97 88.1% 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 Mon Oct 10 2011 at 19:32:10 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 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: 2.733788 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): -34.13300 21.60100 ymin,ymax (A): 39.28800 88.28400 zmin,zma (A): 0.1240000 58.72400 x,y,z range (A): 55.73400 48.99599 58.60000 scale (grids/A): 2.733788 object centre (A): -6.266002 63.78600 29.42400 number of atom coordinates read : 2899 total number of charged atoms : 2757 net assigned charge : 0.5000129 assigned positive charge : 439.5302 centred at (gu) : 100.0429 88.39137 84.84588 assigned negative charge : -439.0310 centred at (gu) : 99.76984 88.29339 84.93275 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 176996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25578 grid for indexing accessible points = 1.400000 m= 84794 mr = 127150 m= 27891 mr = 67545 m= 5655 mr = 21610 m= 539 mr = 3763 m= 19 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 75565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 22054 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) : 1.822526 object centre at (A) : -6.266002 63.78600 29.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4546162E-03 -0.9861250 midg,1,midg; midg,igrid,midg -1.0961319E-03 0.1291520 1,midg,midg; igrid,midg,midg -5.9784245E-02 4.7557909E-02 gauss-seidel spectral radius is 0.9992416 estimated iterations to convergence 287 setup time was (sec) 1.750000 now iterating at: 19:32:12 rms-change max change #iterations 10.01842 310.0793 at 10iterations 5.807201 124.0113 at 20iterations 3.341181 63.34827 at 30iterations 1.920983 39.37434 at 40iterations 1.101727 21.21162 at 50iterations 0.6299496 12.15808 at 60iterations 0.3599750 6.949128 at 70iterations 0.2056725 4.147852 at 80iterations 0.1173740 2.402996 at 90iterations 6.7104608E-02 1.402508 at 100iterations 3.8302839E-02 0.6749725 at 110iterations 2.1836562E-02 0.4174557 at 120iterations 1.2479640E-02 0.2202368 at 130iterations 7.1172868E-03 0.1309214 at 140iterations 4.0706028E-03 8.6585045E-02 at 150iterations 2.3292438E-03 4.2686462E-02 at 160iterations 1.3389961E-03 2.4139404E-02 at 170iterations 7.7261036E-04 1.3732910E-02 at 180iterations finished qdiffx linear iterations at : 19:32:22 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 7.7261036E-04 1.3732910E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 19:32:23 12.462u 0.211s 0:13.16 96.2% 0+0k 0+0io 0pf+0w