Mon Oct 10 19:32:23 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 Mon Oct 10 2011 at 19:32:23 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: HIT 150 has a net charge of 0.5140 !!! 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 : 0.5140110 assigned positive charge : 443.9723 centred at (gu) : 92.24348 89.61182 88.85679 assigned negative charge : -443.4590 centred at (gu) : 92.18182 89.58389 88.88261 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 = 0.1700000 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 = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 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 0.5000000 number of grid points assigned charge 8762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9840676E-09 -8.9287350E-10 midg,1,midg; midg,igrid,midg -1.3920536E-09 1.5004230E-09 1,midg,midg; igrid,midg,midg -1.8323131E-09 5.6690275E-09 gauss-seidel spectral radius is 0.9859994 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 19:32:24 rms-change max change #iterations 0.1237123 17.64622 at 10iterations 1.0804753E-02 1.630116 at 20iterations 9.4697898E-04 0.1308517 at 30iterations 8.4914071E-05 1.2892723E-02 at 40iterations 8.3317800E-06 1.1024475E-03 at 50iterations finished qdiffx linear iterations at : 19:32:27 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 8.3317800E-06 1.1024475E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 19:32:28 3.548u 0.153s 0:04.47 82.5% 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 19:32:28 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: HIT 150 has a net charge of 0.5140 !!! 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 : 0.5140110 assigned positive charge : 443.9723 centred at (gu) : 96.72975 88.83450 86.56964 assigned negative charge : -443.4590 centred at (gu) : 96.54502 88.75098 86.64727 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 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 0.5700000 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 0.7200000 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 5.4722833E-03 -5.3641547E-02 midg,1,midg; midg,igrid,midg -1.1505947E-05 8.9294175E-03 1,midg,midg; igrid,midg,midg -8.9232912E-03 8.4563401E-03 gauss-seidel spectral radius is 0.9985390 estimated iterations to convergence 207 setup time was (sec) 0.8900000 now iterating at: 19:32:29 rms-change max change #iterations 4.267871 168.4009 at 10iterations 1.949940 64.17610 at 20iterations 0.8902425 28.22669 at 30iterations 0.4055680 13.64969 at 40iterations 0.1853237 6.452286 at 50iterations 8.4547289E-02 2.735981 at 60iterations 3.8541880E-02 1.198843 at 70iterations 1.7579021E-02 0.5924902 at 80iterations 8.0308691E-03 0.2544069 at 90iterations 3.6546569E-03 0.1370754 at 100iterations 1.6779542E-03 5.1483154E-02 at 110iterations 7.6508510E-04 2.4782181E-02 at 120iterations finished qdiffx linear iterations at : 19:32:35 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 7.6508510E-04 2.4782181E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 19:32:36 7.604u 0.196s 0:08.27 94.1% 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 19:32:36 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: HIT 150 has a net charge of 0.5140 !!! 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: 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 : 0.5140110 assigned positive charge : 443.9723 centred at (gu) : 100.0942 88.25165 84.85428 assigned negative charge : -443.4590 centred at (gu) : 99.81747 88.12646 84.97083 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 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 = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 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 1.620000 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 2.0517591E-02 -0.9826292 midg,1,midg; midg,igrid,midg -2.2538774E-02 0.1332429 1,midg,midg; igrid,midg,midg -6.1687905E-02 5.0345089E-02 gauss-seidel spectral radius is 0.9992416 estimated iterations to convergence 287 setup time was (sec) 1.790000 now iterating at: 19:32:38 rms-change max change #iterations 10.15184 310.0790 at 10iterations 5.883150 134.8834 at 20iterations 3.383940 64.31370 at 30iterations 1.945278 40.29317 at 40iterations 1.115638 20.98924 at 50iterations 0.6376460 12.14014 at 60iterations 0.3643527 7.037353 at 70iterations 0.2081229 4.151455 at 80iterations 0.1187600 2.379059 at 90iterations 6.7872524E-02 1.396472 at 100iterations 3.8716532E-02 0.7061768 at 110iterations 2.2073872E-02 0.4178886 at 120iterations 1.2610752E-02 0.2151670 at 130iterations 7.1847625E-03 0.1312490 at 140iterations 4.1017318E-03 8.7856293E-02 at 150iterations 2.3410644E-03 4.3540955E-02 at 160iterations 1.3396733E-03 2.3162842E-02 at 170iterations 7.6695340E-04 1.3999939E-02 at 180iterations finished qdiffx linear iterations at : 19:32:49 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 7.6695340E-04 1.3999939E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 19:32:50 12.807u 0.185s 0:13.75 94.4% 0+0k 0+0io 0pf+0w