Sat Oct 15 14:55:32 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 15 2011 at 14:55:32 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: HIR 613 has a net charge of 0.5140 !!! WARNING: GLM 817 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6309149 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): -31.03000 25.39600 ymin,ymax (A): 29.34200 83.04200 zmin,zma (A): 60.58900 108.5910 x,y,z range (A): 56.42600 53.70000 48.00200 scale (grids/A): 0.6309149 object centre (A): -2.816999 56.19200 84.59000 number of atom coordinates read : 2746 total number of charged atoms : 2601 net assigned charge : 3.920026 assigned positive charge : 413.3246 centred at (gu) : 88.40991 91.99638 90.13651 assigned negative charge : -409.4056 centred at (gu) : 88.52098 92.05502 90.17786 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7148 nv = 96 ne = 84 npr = 56627 no. pairs analyzed = 56627 no. exposed pairs = 3473 no. arc points = 24004 no. surface atoms = 1172 nbur = 1574 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3818 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2385 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8756 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9749860E-09 3.5501760E-10 midg,1,midg; midg,igrid,midg 6.4271179E-09 -2.2116839E-09 1,midg,midg; igrid,midg,midg 2.0883586E-08 -4.4506314E-09 gauss-seidel spectral radius is 0.9869980 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 14:55:32 rms-change max change #iterations 0.1409737 26.44580 at 10iterations 1.3504789E-02 1.757516 at 20iterations 1.3066963E-03 0.1764755 at 30iterations 1.3481284E-04 2.0471573E-02 at 40iterations 1.7771161E-05 2.6202202E-03 at 50iterations finished qdiffx linear iterations at : 14:55:38 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.7771161E-05 2.6202202E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 14:55:38 3.509u 0.192s 0:06.60 55.9% 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 15 2011 at 14:55:39 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: HIR 613 has a net charge of 0.5140 !!! WARNING: GLM 817 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.892745 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): -31.03000 25.39600 ymin,ymax (A): 29.34200 83.04200 zmin,zma (A): 60.58900 108.5910 x,y,z range (A): 56.42600 53.70000 48.00200 scale (grids/A): 1.892745 object centre (A): -2.816999 56.19200 84.59000 number of atom coordinates read : 2746 total number of charged atoms : 2601 net assigned charge : 3.920026 assigned positive charge : 413.3246 centred at (gu) : 85.22903 95.98867 90.40918 assigned negative charge : -409.4056 centred at (gu) : 85.56274 96.16511 90.53340 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24004 grid for indexing accessible points = 1.400000 m= 27210 mr = 53124 m= 4321 mr = 19335 m= 237 mr = 2414 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 0.3800000 number of dielectric boundary points 34307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20443 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) : 0.6309149 object centre at (A) : -2.816999 56.19200 84.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0874256E-02 5.6924135E-03 midg,1,midg; midg,igrid,midg 1.4550650E-02 -7.9347668E-03 1,midg,midg; igrid,midg,midg 4.0717177E-02 8.1114406E-03 gauss-seidel spectral radius is 0.9986297 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 14:55:39 rms-change max change #iterations 4.362654 182.5853 at 10iterations 2.033126 64.71529 at 20iterations 0.9499906 37.69107 at 30iterations 0.4462700 15.21799 at 40iterations 0.2086017 7.035414 at 50iterations 9.7795703E-02 3.126507 at 60iterations 4.5564312E-02 1.497604 at 70iterations 2.1346256E-02 0.6843967 at 80iterations 9.9900030E-03 0.3296390 at 90iterations 4.6823374E-03 0.1414986 at 100iterations 2.1931774E-03 7.2511435E-02 at 110iterations 1.0273373E-03 3.2174468E-02 at 120iterations finished qdiffx linear iterations at : 14:55:48 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 1.0273373E-03 3.2174468E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 14:55:49 8.278u 0.227s 0:10.29 82.5% 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 Sat Oct 15 2011 at 14:55:49 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: HIR 613 has a net charge of 0.5140 !!! WARNING: GLM 817 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.839117 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): -31.03000 25.39600 ymin,ymax (A): 29.34200 83.04200 zmin,zma (A): 60.58900 108.5910 x,y,z range (A): 56.42600 53.70000 48.00200 scale (grids/A): 2.839117 object centre (A): -2.816999 56.19200 84.59000 number of atom coordinates read : 2746 total number of charged atoms : 2601 net assigned charge : 3.920026 assigned positive charge : 413.3246 centred at (gu) : 82.84356 98.98301 90.61352 assigned negative charge : -409.4056 centred at (gu) : 83.34412 99.24754 90.80000 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24004 grid for indexing accessible points = 1.400000 m= 88119 mr = 129829 m= 32079 mr = 70399 m= 7749 mr = 24880 m= 995 mr = 5454 m= 73 mr = 532 m= 0 mr = 40 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 895 time to turn everything in is 1.020000 number of dielectric boundary points 77293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 20791 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) : 1.892745 object centre at (A) : -2.816999 56.19200 84.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3290063E-02 5.1568002E-02 midg,1,midg; midg,igrid,midg 0.2229252 -0.1554681 1,midg,midg; igrid,midg,midg 0.5025917 7.2293103E-02 gauss-seidel spectral radius is 0.9992635 estimated iterations to convergence 291 setup time was (sec) 1.280000 now iterating at: 14:55:50 rms-change max change #iterations 10.31982 318.4836 at 10iterations 6.068119 162.2587 at 20iterations 3.540474 98.53176 at 30iterations 2.062120 40.62080 at 40iterations 1.198229 21.30676 at 50iterations 0.6957947 17.76997 at 60iterations 0.4022356 8.715761 at 70iterations 0.2322972 4.042562 at 80iterations 0.1342398 2.326513 at 90iterations 7.7450335E-02 1.553150 at 100iterations 4.4614676E-02 0.7665019 at 110iterations 2.5722511E-02 0.4353600 at 120iterations 1.4826437E-02 0.2658501 at 130iterations 8.5381353E-03 0.1593826 at 140iterations 4.9190954E-03 9.1022491E-02 at 150iterations 2.8259058E-03 5.2243233E-02 at 160iterations 1.6268727E-03 3.0532837E-02 at 170iterations 9.3753467E-04 1.6573906E-02 at 180iterations finished qdiffx linear iterations at : 14:56:03 total time elapsed so far: 13.55000 # loops : 180 mean,max change (kT/e) : 9.3753467E-04 1.6573906E-02 energy calculations done at 13.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.69000 DelPhi exited at 14:56:03 13.687u 0.263s 0:14.24 97.8% 0+0k 0+0io 0pf+0w