Sun Oct 9 11:13:59 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 11:13:59 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 0.6382216 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): -25.68900 24.82700 ymin,ymax (A): -30.62000 25.16000 zmin,zma (A): -1.897000 45.30500 x,y,z range (A): 50.51600 55.78000 47.20200 scale (grids/A): 0.6382216 object centre (A): -0.4310007 -2.730000 21.70400 number of atom coordinates read : 2392 total number of charged atoms : 2269 net assigned charge : -1.485981 assigned positive charge : 347.9409 centred at (gu) : 91.30602 92.17982 89.16087 assigned negative charge : -349.4280 centred at (gu) : 91.26326 92.24350 89.36535 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6873 nv = 96 ne = 84 npr = 46902 no. pairs analyzed = 46902 no. exposed pairs = 3499 no. arc points = 24566 no. surface atoms = 1172 nbur = 1220 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 3391 m= 0 mr = 41 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1350768E-08 -1.9065874E-08 midg,1,midg; midg,igrid,midg 2.5685953E-09 -1.3664593E-08 1,midg,midg; igrid,midg,midg -4.8267990E-09 2.8588059E-09 gauss-seidel spectral radius is 0.9872789 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 11:14:00 rms-change max change #iterations 0.1349802 19.06873 at 10iterations 1.3154069E-02 2.143349 at 20iterations 1.3169181E-03 0.1774189 at 30iterations 1.3622844E-04 2.5592327E-02 at 40iterations 1.8614333E-05 3.7307739E-03 at 50iterations finished qdiffx linear iterations at : 11:14:03 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.8614333E-05 3.7307739E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 11:14:03 3.337u 0.192s 0:03.86 91.1% 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 Sun Oct 9 2011 at 11:14:03 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 1.914665 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): -25.68900 24.82700 ymin,ymax (A): -30.62000 25.16000 zmin,zma (A): -1.897000 45.30500 x,y,z range (A): 50.51600 55.78000 47.20200 scale (grids/A): 1.914665 object centre (A): -0.4310007 -2.730000 21.70400 number of atom coordinates read : 2392 total number of charged atoms : 2269 net assigned charge : -1.485981 assigned positive charge : 347.9409 centred at (gu) : 93.91766 96.53880 87.48194 assigned negative charge : -349.4280 centred at (gu) : 93.78983 96.73068 88.09607 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24566 grid for indexing accessible points = 1.400000 m= 25946 mr = 47966 m= 4488 mr = 18067 m= 280 mr = 2598 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 491 time to turn everything in is 0.5500000 number of dielectric boundary points 35181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17863 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) : 0.6382216 object centre at (A) : -0.4310007 -2.730000 21.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0930154E-02 -1.8370163E-02 midg,1,midg; midg,igrid,midg 2.5661236E-03 -2.3753921E-02 1,midg,midg; igrid,midg,midg -8.5209170E-03 1.0620997E-02 gauss-seidel spectral radius is 0.9986498 estimated iterations to convergence 216 setup time was (sec) 0.8500000 now iterating at: 11:14:04 rms-change max change #iterations 4.053760 156.1601 at 10iterations 1.894154 67.93119 at 20iterations 0.8908612 32.66553 at 30iterations 0.4170628 12.62328 at 40iterations 0.1959271 7.044674 at 50iterations 9.1716923E-02 2.870888 at 60iterations 4.3147121E-02 1.376194 at 70iterations 2.0262539E-02 0.6495552 at 80iterations 9.5417965E-03 0.2960358 at 90iterations 4.4757067E-03 0.1415634 at 100iterations 2.1049671E-03 6.7968369E-02 at 110iterations 9.8954386E-04 3.2747269E-02 at 120iterations finished qdiffx linear iterations at : 11:14:11 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 9.8954386E-04 3.2747269E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 11:14:11 7.625u 0.218s 0:08.18 95.7% 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 Sun Oct 9 2011 at 11:14:11 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 2.871997 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): -25.68900 24.82700 ymin,ymax (A): -30.62000 25.16000 zmin,zma (A): -1.897000 45.30500 x,y,z range (A): 50.51600 55.78000 47.20200 scale (grids/A): 2.871997 object centre (A): -0.4310007 -2.730000 21.70400 number of atom coordinates read : 2392 total number of charged atoms : 2269 net assigned charge : -1.485981 assigned positive charge : 347.9409 centred at (gu) : 95.87624 99.80801 86.22289 assigned negative charge : -349.4280 centred at (gu) : 95.68463 100.0959 87.14397 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 168876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24566 grid for indexing accessible points = 1.400000 m= 82636 mr = 117386 m= 31237 mr = 64903 m= 8052 mr = 24039 m= 1204 mr = 5675 m= 57 mr = 744 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 1707 time to turn everything in is 1.340000 number of dielectric boundary points 79305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 18150 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) : 1.914665 object centre at (A) : -0.4310007 -2.730000 21.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2002475 -0.1609604 midg,1,midg; midg,igrid,midg 5.7055630E-02 -0.2117818 1,midg,midg; igrid,midg,midg -0.1711415 0.1103909 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.670000 now iterating at: 11:14:13 rms-change max change #iterations 9.697635 351.7665 at 10iterations 5.749665 135.4062 at 20iterations 3.400663 77.55569 at 30iterations 2.003294 43.94574 at 40iterations 1.174963 22.26310 at 50iterations 0.6840429 13.85099 at 60iterations 0.3989470 7.469383 at 70iterations 0.2317486 4.493919 at 80iterations 0.1345019 2.576187 at 90iterations 7.7973574E-02 1.426012 at 100iterations 4.5272864E-02 0.8568449 at 110iterations 2.6170654E-02 0.5077248 at 120iterations 1.5158780E-02 0.2552357 at 130iterations 8.7609412E-03 0.1636925 at 140iterations 5.0617801E-03 9.3191624E-02 at 150iterations 2.9254858E-03 5.2522659E-02 at 160iterations 1.6919232E-03 3.2817841E-02 at 170iterations 9.7825192E-04 2.0065308E-02 at 180iterations finished qdiffx linear iterations at : 11:14:24 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 9.7825192E-04 2.0065308E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 11:14:25 12.607u 0.234s 0:13.19 97.2% 0+0k 0+0io 0pf+0w