Tue Oct 11 07:50:46 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 Tue Oct 11 2011 at 07:50:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6416727 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): -13.17900 42.30100 ymin,ymax (A): -22.36500 25.33300 zmin,zma (A): -5.379000 40.33800 x,y,z range (A): 55.48000 47.69800 45.71700 scale (grids/A): 0.6416727 object centre (A): 14.56100 1.484000 17.47950 number of atom coordinates read : 2733 total number of charged atoms : 2372 net assigned charge : 8.500014 assigned positive charge : 380.0450 centred at (gu) : 89.93492 88.79068 89.11998 assigned negative charge : -371.5457 centred at (gu) : 89.94813 88.75633 89.27368 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 51214 no. pairs analyzed = 51214 no. exposed pairs = 2922 no. arc points = 20393 no. surface atoms = 1004 nbur = 1729 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3863 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2025 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6790428E-08 -4.3387574E-09 midg,1,midg; midg,igrid,midg 1.1262780E-08 1.3106565E-08 1,midg,midg; igrid,midg,midg 1.4580023E-08 1.1154350E-08 gauss-seidel spectral radius is 0.9874011 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 07:50:47 rms-change max change #iterations 0.1427198 21.59167 at 10iterations 1.4657656E-02 2.001427 at 20iterations 1.7097547E-03 0.2920074 at 30iterations 2.5147171E-04 3.6094666E-02 at 40iterations 4.7991802E-05 7.1601868E-03 at 50iterations finished qdiffx linear iterations at : 07:50:50 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 4.7991802E-05 7.1601868E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 07:50:50 3.131u 0.137s 0:03.84 84.8% 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 Tue Oct 11 2011 at 07:50:50 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 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: 1.925018 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): -13.17900 42.30100 ymin,ymax (A): -22.36500 25.33300 zmin,zma (A): -5.379000 40.33800 x,y,z range (A): 55.48000 47.69800 45.71700 scale (grids/A): 1.925018 object centre (A): 14.56100 1.484000 17.47950 number of atom coordinates read : 2733 total number of charged atoms : 2372 net assigned charge : 8.500014 assigned positive charge : 380.0450 centred at (gu) : 89.80428 86.37154 87.35936 assigned negative charge : -371.5457 centred at (gu) : 89.84439 86.26893 87.82108 start vw surface at 0.2400000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 73099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20393 grid for indexing accessible points = 1.400000 m= 26525 mr = 51939 m= 3844 mr = 19883 m= 210 mr = 2303 m= 6 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 29476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18624 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) : 0.6416727 object centre at (A) : 14.56100 1.484000 17.47950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3302123E-02 -2.0846594E-03 midg,1,midg; midg,igrid,midg 8.8966368E-03 2.1142621E-02 1,midg,midg; igrid,midg,midg 2.1308025E-02 3.7597701E-02 gauss-seidel spectral radius is 0.9986465 estimated iterations to convergence 215 setup time was (sec) 0.8700000 now iterating at: 07:50:51 rms-change max change #iterations 4.212625 182.8932 at 10iterations 1.986063 71.53117 at 20iterations 0.9311024 35.14038 at 30iterations 0.4407967 13.43471 at 40iterations 0.2084588 6.524612 at 50iterations 9.7825572E-02 3.120363 at 60iterations 4.6361104E-02 1.561491 at 70iterations 2.1900380E-02 0.7247353 at 80iterations 1.0348344E-02 0.3159342 at 90iterations 4.9322862E-03 0.1612988 at 100iterations 2.3637270E-03 7.1165085E-02 at 110iterations 1.1465291E-03 4.0760040E-02 at 120iterations finished qdiffx linear iterations at : 07:50:58 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.1465291E-03 4.0760040E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 07:50:59 7.479u 0.187s 0:08.28 92.3% 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 Tue Oct 11 2011 at 07:50:59 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 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: 2.887527 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): -13.17900 42.30100 ymin,ymax (A): -22.36500 25.33300 zmin,zma (A): -5.379000 40.33800 x,y,z range (A): 55.48000 47.69800 45.71700 scale (grids/A): 2.887527 object centre (A): 14.56100 1.484000 17.47950 number of atom coordinates read : 2733 total number of charged atoms : 2372 net assigned charge : 8.500014 assigned positive charge : 380.0450 centred at (gu) : 89.70631 84.55727 86.03893 assigned negative charge : -371.5457 centred at (gu) : 89.76656 84.40338 86.73159 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 168884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20393 grid for indexing accessible points = 1.400000 m= 86364 mr = 124949 m= 30407 mr = 71893 m= 6795 mr = 24473 m= 967 mr = 5029 m= 55 mr = 661 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 66444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 18970 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) : 1.925018 object centre at (A) : 14.56100 1.484000 17.47950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4003832 -8.1050307E-02 midg,1,midg; midg,igrid,midg 7.7669628E-02 0.2267630 1,midg,midg; igrid,midg,midg 9.5028579E-02 0.2929492 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 1.710000 now iterating at: 07:51:01 rms-change max change #iterations 9.685205 332.0809 at 10iterations 5.596005 117.0395 at 20iterations 3.228257 62.87920 at 30iterations 1.858018 39.48742 at 40iterations 1.065592 22.40251 at 50iterations 0.6132216 12.80506 at 60iterations 0.3518417 6.357051 at 70iterations 0.2014726 3.522655 at 80iterations 0.1155006 2.167253 at 90iterations 6.6192649E-02 1.309697 at 100iterations 3.7923165E-02 0.7270861 at 110iterations 2.1790551E-02 0.3861103 at 120iterations 1.2524301E-02 0.2318687 at 130iterations 7.2323130E-03 0.1467571 at 140iterations 4.2030602E-03 7.7141762E-02 at 150iterations 2.4797218E-03 4.7027588E-02 at 160iterations 1.4891438E-03 3.0200005E-02 at 170iterations 9.2035148E-04 1.8085480E-02 at 180iterations finished qdiffx linear iterations at : 07:51:12 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 9.2035148E-04 1.8085480E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 07:51:13 13.178u 0.251s 0:14.02 95.7% 0+0k 0+0io 0pf+0w