Sat Oct 8 20:36:39 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 Sat Oct 8 2011 at 20:36:39 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN2 264 has a net charge of 1.4000 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: 0.6241124 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): -32.32000 17.45500 ymin,ymax (A): -24.34200 22.68300 zmin,zma (A): -12.37200 44.66900 x,y,z range (A): 49.77500 47.02500 57.04100 scale (grids/A): 0.6241124 object centre (A): -7.432500 -0.8294992 16.14850 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 88.68316 89.24361 89.77860 assigned negative charge : -388.6046 centred at (gu) : 88.58296 89.28277 89.66010 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6628 nv = 96 ne = 84 npr = 54338 no. pairs analyzed = 54338 no. exposed pairs = 2990 no. arc points = 21297 no. surface atoms = 1005 nbur = 1589 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3769 m= 0 mr = 54 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.3500000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2133 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8144 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4934559E-09 1.1908307E-08 midg,1,midg; midg,igrid,midg 7.8675342E-09 7.1962569E-10 1,midg,midg; igrid,midg,midg -5.2110694E-09 8.3838350E-09 gauss-seidel spectral radius is 0.9866992 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 20:36:40 rms-change max change #iterations 0.1320743 18.90777 at 10iterations 1.2345012E-02 1.880110 at 20iterations 1.1690320E-03 0.2036591 at 30iterations 1.0863773E-04 1.4925003E-02 at 40iterations 1.0193125E-05 1.4123917E-03 at 50iterations finished qdiffx linear iterations at : 20:36:44 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.0193125E-05 1.4123917E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 20:36:44 4.076u 0.253s 0:04.59 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 Sat Oct 8 2011 at 20:36:44 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN2 264 has a net charge of 1.4000 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: 1.872337 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): -32.32000 17.45500 ymin,ymax (A): -24.34200 22.68300 zmin,zma (A): -12.37200 44.66900 x,y,z range (A): 49.77500 47.02500 57.04100 scale (grids/A): 1.872337 object centre (A): -7.432500 -0.8294992 16.14850 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 86.04911 87.73024 89.33543 assigned negative charge : -388.6046 centred at (gu) : 85.74843 87.84819 88.98029 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21297 grid for indexing accessible points = 1.400000 m= 26257 mr = 50995 m= 3883 mr = 19786 m= 183 mr = 2449 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 7900 time to turn everything in is 0.6500000 number of dielectric boundary points 29238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19262 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) : 0.6241124 object centre at (A) : -7.432500 -0.8294992 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6995065E-02 2.2305161E-02 midg,1,midg; midg,igrid,midg 1.0202160E-02 4.3339375E-03 1,midg,midg; igrid,midg,midg -5.8540171E-03 3.6545515E-02 gauss-seidel spectral radius is 0.9985850 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 20:36:45 rms-change max change #iterations 4.110489 166.6107 at 10iterations 1.898257 71.83932 at 20iterations 0.8789410 26.99900 at 30iterations 0.4027328 14.38146 at 40iterations 0.1877031 6.343527 at 50iterations 8.6618394E-02 2.535372 at 60iterations 4.0046904E-02 1.349089 at 70iterations 1.8520439E-02 0.5776405 at 80iterations 8.5585304E-03 0.2987378 at 90iterations 3.9568869E-03 0.1322174 at 100iterations 1.8246843E-03 5.9791565E-02 at 110iterations 8.4475853E-04 2.8301239E-02 at 120iterations finished qdiffx linear iterations at : 20:36:54 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 8.4475853E-04 2.8301239E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 20:36:54 9.373u 0.264s 0:09.90 97.2% 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 20:36:54 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN2 264 has a net charge of 1.4000 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: 2.808506 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): -32.32000 17.45500 ymin,ymax (A): -24.34200 22.68300 zmin,zma (A): -12.37200 44.66900 x,y,z range (A): 49.77500 47.02500 57.04100 scale (grids/A): 2.808506 object centre (A): -7.432500 -0.8294992 16.14850 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 84.07346 86.59539 89.00299 assigned negative charge : -388.6046 centred at (gu) : 83.62263 86.77219 88.47023 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 166897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21297 grid for indexing accessible points = 1.400000 m= 85740 mr = 122804 m= 30138 mr = 71307 m= 7062 mr = 24587 m= 881 mr = 5432 m= 41 mr = 579 m= 0 mr = 8 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 26453 time to turn everything in is 1.600000 number of dielectric boundary points 66042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 19631 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) : 1.872337 object centre at (A) : -7.432500 -0.8294992 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1515628 0.2615288 midg,1,midg; midg,igrid,midg 0.1312686 4.3103941E-02 1,midg,midg; igrid,midg,midg -4.3854658E-02 0.4377236 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 1.920000 now iterating at: 20:36:56 rms-change max change #iterations 9.567182 280.4079 at 10iterations 5.503632 138.6395 at 20iterations 3.153192 69.81068 at 30iterations 1.802069 38.65765 at 40iterations 1.030711 21.58994 at 50iterations 0.5865575 11.69994 at 60iterations 0.3348117 6.571121 at 70iterations 0.1912325 3.432356 at 80iterations 0.1091567 2.060852 at 90iterations 6.2089436E-02 1.218538 at 100iterations 3.5429463E-02 0.7887554 at 110iterations 2.0171622E-02 0.3460703 at 120iterations 1.1477456E-02 0.2008820 at 130iterations 6.5486529E-03 0.1327248 at 140iterations 3.7378608E-03 9.1487885E-02 at 150iterations 2.1303738E-03 4.4388771E-02 at 160iterations 1.2117506E-03 2.2167206E-02 at 170iterations 6.9276034E-04 1.2769699E-02 at 180iterations finished qdiffx linear iterations at : 20:37:10 total time elapsed so far: 15.39000 # loops : 180 mean,max change (kT/e) : 6.9276034E-04 1.2769699E-02 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.56000 DelPhi exited at 20:37:10 15.566u 0.317s 0:16.15 98.2% 0+0k 0+0io 0pf+0w