Sat Oct 8 17:25:46 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 Sat Oct 8 2011 at 17:25:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3480 !!! WARNING: ASN 385 has a net charge of 0.5000 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: 0.5599685 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): 36.07000 95.07800 ymin,ymax (A): 17.00100 80.57600 zmin,zma (A): -21.95600 25.40100 x,y,z range (A): 59.00800 63.57500 47.35700 scale (grids/A): 0.5599685 object centre (A): 65.57401 48.78850 1.722499 number of atom coordinates read : 3480 total number of charged atoms : 3333 net assigned charge : -6.999966 assigned positive charge : 521.8460 centred at (gu) : 90.50953 89.88815 89.48434 assigned negative charge : -528.8478 centred at (gu) : 90.56194 89.85327 89.41852 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7210 nv = 96 ne = 84 npr = 69567 no. pairs analyzed = 69567 no. exposed pairs = 4510 no. arc points = 30355 no. surface atoms = 1509 nbur = 1971 mkacc time = 0.1600000 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= 318 mr = 3865 m= 0 mr = 10 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3068 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9234 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8207966E-09 1.0715100E-10 midg,1,midg; midg,igrid,midg -1.2273905E-09 -2.6983910E-10 1,midg,midg; igrid,midg,midg -4.6217700E-11 -1.6148725E-09 gauss-seidel spectral radius is 0.9835881 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 17:25:47 rms-change max change #iterations 9.2590936E-02 13.46655 at 10iterations 6.6771652E-03 0.9294798 at 20iterations 5.0436822E-04 0.1068153 at 30iterations 6.0052975E-05 9.3408823E-03 at 40iterations 1.4168669E-05 2.2470951E-03 at 50iterations finished qdiffx linear iterations at : 17:25:50 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 1.4168669E-05 2.2470951E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 17:25:51 4.288u 0.228s 0:04.80 93.7% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 17:25:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3480 !!! WARNING: ASN 385 has a net charge of 0.5000 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: 1.679906 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): 36.07000 95.07800 ymin,ymax (A): 17.00100 80.57600 zmin,zma (A): -21.95600 25.40100 x,y,z range (A): 59.00800 63.57500 47.35700 scale (grids/A): 1.679906 object centre (A): 65.57401 48.78850 1.722499 number of atom coordinates read : 3480 total number of charged atoms : 3333 net assigned charge : -6.999966 assigned positive charge : 521.8460 centred at (gu) : 91.52802 89.66342 88.45214 assigned negative charge : -528.8478 centred at (gu) : 91.68536 89.55925 88.25489 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30355 grid for indexing accessible points = 1.400000 m= 27308 mr = 54753 m= 3255 mr = 19277 m= 104 mr = 1713 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 509 time to turn everything in is 0.5900000 number of dielectric boundary points 33920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 25627 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) : 0.5599685 object centre at (A) : 65.57401 48.78850 1.722499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3262212E-02 -1.0948343E-03 midg,1,midg; midg,igrid,midg 3.6135965E-03 2.0645654E-02 1,midg,midg; igrid,midg,midg -1.3944713E-02 -1.5554003E-02 gauss-seidel spectral radius is 0.9983387 estimated iterations to convergence 195 setup time was (sec) 0.9300000 now iterating at: 17:25:52 rms-change max change #iterations 3.882036 163.6989 at 10iterations 1.676995 54.72772 at 20iterations 0.7257320 27.69571 at 30iterations 0.3142078 10.57363 at 40iterations 0.1363410 4.395470 at 50iterations 5.8948476E-02 2.077719 at 60iterations 2.5632473E-02 0.7987454 at 70iterations 1.1141255E-02 0.3648987 at 80iterations 4.8328466E-03 0.1599998 at 90iterations 2.1041115E-03 6.8933487E-02 at 100iterations 9.2139945E-04 2.6466370E-02 at 110iterations 4.0709789E-04 1.3009071E-02 at 120iterations finished qdiffx linear iterations at : 17:26:01 total time elapsed so far: 9.690000 # loops : 120 mean,max change (kT/e) : 4.0709789E-04 1.3009071E-02 energy calculations done at 9.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.870000 DelPhi exited at 17:26:01 9.869u 0.259s 0:10.45 96.7% 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 Sat Oct 8 2011 at 17:26:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3480 !!! WARNING: ASN 385 has a net charge of 0.5000 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: 2.519858 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): 36.07000 95.07800 ymin,ymax (A): 17.00100 80.57600 zmin,zma (A): -21.95600 25.40100 x,y,z range (A): 59.00800 63.57500 47.35700 scale (grids/A): 2.519858 object centre (A): 65.57401 48.78850 1.722499 number of atom coordinates read : 3480 total number of charged atoms : 3333 net assigned charge : -6.999966 assigned positive charge : 521.8460 centred at (gu) : 92.29173 89.49497 87.67775 assigned negative charge : -528.8478 centred at (gu) : 92.52799 89.33871 87.38215 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 183140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30355 grid for indexing accessible points = 1.400000 m= 91431 mr = 133327 m= 28543 mr = 73409 m= 5147 mr = 21950 m= 451 mr = 3458 m= 15 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1726 time to turn everything in is 1.470000 number of dielectric boundary points 76406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 26644 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) : 1.679906 object centre at (A) : 65.57401 48.78850 1.722499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1744020 2.3351902E-02 midg,1,midg; midg,igrid,midg 0.3931504 0.6276729 1,midg,midg; igrid,midg,midg -0.1498434 -0.1383583 gauss-seidel spectral radius is 0.9991942 estimated iterations to convergence 278 setup time was (sec) 1.820000 now iterating at: 17:26:03 rms-change max change #iterations 9.869486 284.4191 at 10iterations 5.660410 132.8615 at 20iterations 3.233238 73.01967 at 30iterations 1.836959 38.84705 at 40iterations 1.042590 22.46243 at 50iterations 0.5881233 11.21322 at 60iterations 0.3325059 6.304365 at 70iterations 0.1870253 3.792603 at 80iterations 0.1054514 2.037698 at 90iterations 5.9227671E-02 1.161373 at 100iterations 3.3300646E-02 0.6213837 at 110iterations 1.8734850E-02 0.3807030 at 120iterations 1.0542735E-02 0.2004087 at 130iterations 5.9200642E-03 0.1030426 at 140iterations 3.3371844E-03 6.3022614E-02 at 150iterations 1.8815121E-03 3.4963131E-02 at 160iterations 1.0712622E-03 2.0393372E-02 at 170iterations 6.1368546E-04 1.0915756E-02 at 180iterations finished qdiffx linear iterations at : 17:26:18 total time elapsed so far: 16.04000 # loops : 180 mean,max change (kT/e) : 6.1368546E-04 1.0915756E-02 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.23000 DelPhi exited at 17:26:18 16.231u 0.293s 0:16.94 97.5% 0+0k 0+0io 0pf+0w