Sun Oct 9 17:24:02 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 Sun Oct 9 2011 at 17:24:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5141 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5480380 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): 3.225000 68.18400 ymin,ymax (A): -8.537000 53.47000 zmin,zma (A): -1.226000 62.04800 x,y,z range (A): 64.95900 62.00700 63.27400 scale (grids/A): 0.5480380 object centre (A): 35.70450 22.46650 30.41100 number of atom coordinates read : 5141 total number of charged atoms : 4990 net assigned charge : -0.3649497 assigned positive charge : 791.9166 centred at (gu) : 87.90855 89.15261 89.28002 assigned negative charge : -792.2877 centred at (gu) : 87.78404 89.17947 89.26606 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10005 nv = 96 ne = 84 npr = 104495 no. pairs analyzed = 104495 no. exposed pairs = 6119 no. arc points = 41235 no. surface atoms = 2082 nbur = 3059 mkacc time = 0.2500000 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 = 1.568000 m= 431 mr = 5641 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4188 ## 487 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13212 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9861100E-10 1.5732914E-10 midg,1,midg; midg,igrid,midg 4.3544512E-10 -2.6760694E-10 1,midg,midg; igrid,midg,midg -2.7117506E-09 9.3343644E-10 gauss-seidel spectral radius is 0.9829869 estimated iterations to convergence 63 setup time was (sec) 0.7600000 now iterating at: 17:24:03 rms-change max change #iterations 0.1057983 13.08220 at 10iterations 9.1622351E-03 1.140671 at 20iterations 2.5572898E-03 0.3047256 at 30iterations 1.2020553E-03 0.1321335 at 40iterations 5.9362064E-04 6.6663742E-02 at 50iterations finished qdiffx linear iterations at : 17:24:05 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 5.9362064E-04 6.6663742E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 17:24:06 3.575u 0.139s 0:04.00 92.5% 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 Sun Oct 9 2011 at 17:24:06 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5141 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.644114 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): 3.225000 68.18400 ymin,ymax (A): -8.537000 53.47000 zmin,zma (A): -1.226000 62.04800 x,y,z range (A): 64.95900 62.00700 63.27400 scale (grids/A): 1.644114 object centre (A): 35.70450 22.46650 30.41100 number of atom coordinates read : 5141 total number of charged atoms : 4990 net assigned charge : -0.3649497 assigned positive charge : 791.9166 centred at (gu) : 83.72429 87.45655 87.83862 assigned negative charge : -792.2877 centred at (gu) : 83.35206 87.53849 87.79823 start vw surface at 0.2100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 111525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38414 mr = 80419 m= 4553 mr = 27572 m= 141 mr = 2384 m= 0 mr = 5 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 44253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 38271 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) : 0.5480380 object centre at (A) : 35.70450 22.46650 30.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9914169E-02 -1.7404845E-02 midg,1,midg; midg,igrid,midg 1.6252361E-02 8.6543700E-03 1,midg,midg; igrid,midg,midg -3.1416930E-02 1.4604979E-02 gauss-seidel spectral radius is 0.9984057 estimated iterations to convergence 199 setup time was (sec) 1.090000 now iterating at: 17:24:07 rms-change max change #iterations 4.739076 178.1069 at 10iterations 2.085495 57.91331 at 20iterations 0.9225956 28.37054 at 30iterations 0.4062957 10.61363 at 40iterations 0.1802828 5.109203 at 50iterations 7.9750285E-02 2.302058 at 60iterations 3.5639353E-02 0.9716492 at 70iterations 1.6167533E-02 0.4677198 at 80iterations 7.7686054E-03 0.2271309 at 90iterations 4.1253171E-03 0.1070404 at 100iterations 2.5195063E-03 6.6284180E-02 at 110iterations 1.7505807E-03 4.4075012E-02 at 120iterations finished qdiffx linear iterations at : 17:24:14 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.7505807E-03 4.4075012E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 17:24:14 7.845u 0.166s 0:08.28 96.6% 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 Sun Oct 9 2011 at 17:24:14 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5141 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.466171 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): 3.225000 68.18400 ymin,ymax (A): -8.537000 53.47000 zmin,zma (A): -1.226000 62.04800 x,y,z range (A): 64.95900 62.00700 63.27400 scale (grids/A): 2.466171 object centre (A): 35.70450 22.46650 30.41100 number of atom coordinates read : 5141 total number of charged atoms : 4990 net assigned charge : -0.3649497 assigned positive charge : 791.9166 centred at (gu) : 80.58611 86.18438 86.75755 assigned negative charge : -792.2877 centred at (gu) : 80.02805 86.30762 86.69745 start vw surface at 0.2200000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 259301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 129688 mr = 195920 m= 40738 mr = 105190 m= 7405 mr = 31455 m= 588 mr = 5033 m= 13 mr = 254 m= 0 mr = 2 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 99879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 39874 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) : 1.644114 object centre at (A) : 35.70450 22.46650 30.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3617016 -0.4030783 midg,1,midg; midg,igrid,midg 7.6165572E-02 -8.1803103E-04 1,midg,midg; igrid,midg,midg -0.5273475 0.1895736 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 2.320000 now iterating at: 17:24:17 rms-change max change #iterations 12.12254 350.7252 at 10iterations 7.133022 140.9951 at 20iterations 4.161176 84.21097 at 30iterations 2.425729 52.70329 at 40iterations 1.404332 24.48133 at 50iterations 0.8126112 13.78695 at 60iterations 0.4694469 7.889199 at 70iterations 0.2706102 4.523918 at 80iterations 0.1558796 2.445853 at 90iterations 8.9730047E-02 1.462212 at 100iterations 5.1806852E-02 0.8048859 at 110iterations 2.9915433E-02 0.5463963 at 120iterations 1.7517073E-02 0.2693787 at 130iterations 1.0429560E-02 0.1765862 at 140iterations 6.4472035E-03 0.1064606 at 150iterations 4.2001014E-03 7.6755524E-02 at 160iterations 2.9451402E-03 4.6770096E-02 at 170iterations 2.2226963E-03 3.4420013E-02 at 180iterations finished qdiffx linear iterations at : 17:24:27 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 2.2226963E-03 3.4420013E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 17:24:28 13.074u 0.176s 0:13.53 97.8% 0+0k 0+0io 0pf+0w