Mon Oct 10 19:32:34 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 Mon Oct 10 2011 at 19:32:34 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 !!! WARNING: HIR 257 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: 0.7166871 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): 25.55500 73.92000 ymin,ymax (A): 16.66600 66.33900 zmin,zma (A): 7.633000 57.06300 x,y,z range (A): 48.36500 49.67300 49.43000 scale (grids/A): 0.7166871 object centre (A): 49.73750 41.50250 32.34800 number of atom coordinates read : 2488 total number of charged atoms : 2351 net assigned charge : 3.014009 assigned positive charge : 376.8938 centred at (gu) : 89.79623 86.83353 88.33599 assigned negative charge : -373.8805 centred at (gu) : 89.71691 86.99538 88.27184 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8484 nv = 96 ne = 84 npr = 52370 no. pairs analyzed = 52370 no. exposed pairs = 2940 no. arc points = 20113 no. surface atoms = 988 nbur = 1500 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4953 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.2900000 number of dielectric boundary points 3984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6164102E-08 5.3810659E-08 midg,1,midg; midg,igrid,midg 2.6703296E-07 -4.7978460E-08 1,midg,midg; igrid,midg,midg -3.0460608E-08 8.1334832E-08 gauss-seidel spectral radius is 0.9898868 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 19:32:34 rms-change max change #iterations 0.2364324 30.12680 at 10iterations 3.0351995E-02 3.608910 at 20iterations 3.8342145E-03 0.4446831 at 30iterations 4.9662514E-04 6.3678741E-02 at 40iterations 6.7245252E-05 8.2368851E-03 at 50iterations finished qdiffx linear iterations at : 19:32:37 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.7245252E-05 8.2368851E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:32:38 3.384u 0.226s 0:04.53 79.4% 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 Mon Oct 10 2011 at 19:32:38 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 !!! WARNING: HIR 257 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.150061 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): 25.55500 73.92000 ymin,ymax (A): 16.66600 66.33900 zmin,zma (A): 7.633000 57.06300 x,y,z range (A): 48.36500 49.67300 49.43000 scale (grids/A): 2.150061 object centre (A): 49.73750 41.50250 32.34800 number of atom coordinates read : 2488 total number of charged atoms : 2351 net assigned charge : 3.014009 assigned positive charge : 376.8938 centred at (gu) : 89.38797 80.50004 85.00753 assigned negative charge : -373.8805 centred at (gu) : 89.15058 80.98591 84.81512 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20113 grid for indexing accessible points = 1.400000 m= 35083 mr = 63535 m= 6667 mr = 26929 m= 550 mr = 4404 m= 20 mr = 292 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2625 time to turn everything in is 0.6200000 number of dielectric boundary points 36708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18693 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) : 0.7166871 object centre at (A) : 49.73750 41.50250 32.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0185752E-02 2.1614548E-02 midg,1,midg; midg,igrid,midg 6.6821054E-02 -1.4801595E-02 1,midg,midg; igrid,midg,midg 7.8836428E-03 2.8630726E-02 gauss-seidel spectral radius is 0.9988853 estimated iterations to convergence 237 setup time was (sec) 0.9000000 now iterating at: 19:32:39 rms-change max change #iterations 5.218956 205.9609 at 10iterations 2.627403 78.59870 at 20iterations 1.322850 42.34225 at 30iterations 0.6672906 19.52276 at 40iterations 0.3375195 9.628605 at 50iterations 0.1699443 4.567126 at 60iterations 8.5727088E-02 3.024751 at 70iterations 4.3210607E-02 1.164448 at 80iterations 2.1829594E-02 0.6541100 at 90iterations 1.1011855E-02 0.3183746 at 100iterations 5.5597425E-03 0.1535244 at 110iterations 2.8124470E-03 7.7550888E-02 at 120iterations finished qdiffx linear iterations at : 19:32:46 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 2.8124470E-03 7.7550888E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 19:32:47 7.625u 0.252s 0:08.25 95.3% 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 Mon Oct 10 2011 at 19:32:47 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 !!! WARNING: HIR 257 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: 3.225092 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): 25.55500 73.92000 ymin,ymax (A): 16.66600 66.33900 zmin,zma (A): 7.633000 57.06300 x,y,z range (A): 48.36500 49.67300 49.43000 scale (grids/A): 3.225092 object centre (A): 49.73750 41.50250 32.34800 number of atom coordinates read : 2488 total number of charged atoms : 2351 net assigned charge : 3.014009 assigned positive charge : 376.8938 centred at (gu) : 89.08182 75.74982 82.51110 assigned negative charge : -373.8805 centred at (gu) : 88.72578 76.47881 82.22272 start vw surface at 0.1300000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 206871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20113 grid for indexing accessible points = 1.400000 m= 109374 mr = 153378 m= 45101 mr = 91333 m= 12445 mr = 37534 m= 2162 mr = 9544 m= 269 mr = 1528 m= 10 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 9102 time to turn everything in is 2.010000 number of dielectric boundary points 82713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 18808 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) : 2.150061 object centre at (A) : 49.73750 41.50250 32.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8183386E-02 0.6308674 midg,1,midg; midg,igrid,midg 0.3493777 -9.8439962E-02 1,midg,midg; igrid,midg,midg 3.2370321E-02 0.1250298 gauss-seidel spectral radius is 0.9993240 estimated iterations to convergence 303 setup time was (sec) 2.330000 now iterating at: 19:32:49 rms-change max change #iterations 11.56753 404.2338 at 10iterations 6.877441 143.8983 at 20iterations 4.087269 89.38054 at 30iterations 2.422735 38.57448 at 40iterations 1.434657 24.98961 at 50iterations 0.8489143 16.30898 at 60iterations 0.5016926 8.234089 at 70iterations 0.2951986 5.183500 at 80iterations 0.1740342 2.654800 at 90iterations 0.1029577 1.554405 at 100iterations 6.0474202E-02 0.9141312 at 110iterations 3.5768408E-02 0.5713272 at 120iterations 2.1007763E-02 0.3181305 at 130iterations 1.2403336E-02 0.1917686 at 140iterations 7.3036873E-03 0.1185074 at 150iterations 4.3015615E-03 6.7792654E-02 at 160iterations 2.5389923E-03 4.1285515E-02 at 170iterations 1.4958364E-03 2.2172928E-02 at 180iterations finished qdiffx linear iterations at : 19:32:59 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 1.4958364E-03 2.2172928E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 19:33:00 12.271u 0.234s 0:13.12 95.2% 0+0k 0+0io 0pf+0w