Sun Oct 9 02:15:28 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 Sun Oct 9 2011 at 02:15:28 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1845 !!! WARNING: HIR 75 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: 0.2340350 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): -114.2920 -61.72100 ymin,ymax (A): -118.3190 33.79500 zmin,zma (A): -2.307000 51.33500 x,y,z range (A): 52.57100 152.1140 53.64200 scale (grids/A): 0.2340350 object centre (A): -88.00650 -42.26200 24.51400 number of atom coordinates read : 1845 total number of charged atoms : 1723 net assigned charge : 6.514015 assigned positive charge : 271.0462 centred at (gu) : 90.65171 76.61819 89.91203 assigned negative charge : -264.5324 centred at (gu) : 90.60874 76.61404 89.93650 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 505 nv = 96 ne = 84 npr = 32120 no. pairs analyzed = 32120 no. exposed pairs = 3174 no. arc points = 22792 no. surface atoms = 1037 nbur = 808 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.640000 m= 10 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 418 no. dielectric boundary points in salt = 1 no. grid points charged and at boundary= 703 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 821 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6212359E-22 7.2460042E-23 midg,1,midg; midg,igrid,midg 3.7610171E-19 2.0840408E-25 1,midg,midg; igrid,midg,midg 7.0715487E-24 4.4891295E-22 gauss-seidel spectral radius is 0.9111066 estimated iterations to convergence 29 setup time was (sec) 0.4500000 now iterating at: 02:15:29 rms-change max change #iterations 4.4782661E-04 0.2467747 at 10iterations 2.5137193E-05 1.3203621E-02 at 20iterations 1.7489228E-06 9.1838837E-04 at 30iterations 1.2107606E-07 6.3419342E-05 at 40iterations 1.0060494E-08 6.6757202E-06 at 50iterations finished qdiffx linear iterations at : 02:15:33 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.0060494E-08 6.6757202E-06 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 02:15:33 4.698u 0.161s 0:05.21 93.0% 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 Sun Oct 9 2011 at 02:15:34 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1845 !!! WARNING: HIR 75 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: 0.7021050 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): -114.2920 -61.72100 ymin,ymax (A): -118.3190 33.79500 zmin,zma (A): -2.307000 51.33500 x,y,z range (A): 52.57100 152.1140 53.64200 scale (grids/A): 0.7021050 object centre (A): -88.00650 -42.26200 24.51400 number of atom coordinates read : 1845 total number of charged atoms : 1723 net assigned charge : 6.514015 assigned positive charge : 271.0462 centred at (gu) : 91.95523 49.85479 89.73620 assigned negative charge : -264.5324 centred at (gu) : 91.82643 49.84244 89.80956 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22792 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.377920 m= 466 mr = 2873 m= 5 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 3.9999992E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1878 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6981 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) : 0.2340350 object centre at (A) : -88.00650 -42.26200 24.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2181542E-08 8.5691703E-08 midg,1,midg; midg,igrid,midg 4.4894061E-04 1.9672369E-10 1,midg,midg; igrid,midg,midg -5.7689270E-08 7.6731105E-08 gauss-seidel spectral radius is 0.9893427 estimated iterations to convergence 79 setup time was (sec) 0.4700000 now iterating at: 02:15:34 rms-change max change #iterations 0.1759415 30.07913 at 10iterations 2.0441614E-02 3.011188 at 20iterations 2.4762480E-03 0.3855772 at 30iterations 3.1977092E-04 4.9868107E-02 at 40iterations 5.6778477E-05 7.7409744E-03 at 50iterations 1.4992911E-05 1.7242432E-03 at 60iterations 4.6450241E-06 4.7874451E-04 at 70iterations 1.4839301E-06 1.5258789E-04 at 80iterations 4.8174627E-07 5.3405762E-05 at 90iterations 1.8054305E-07 3.0517578E-05 at 100iterations 1.0450162E-07 3.0517578E-05 at 110iterations 9.3545260E-08 1.9073486E-05 at 120iterations finished qdiffx linear iterations at : 02:15:40 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 9.3545260E-08 1.9073486E-05 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 02:15:41 6.846u 0.198s 0:07.32 96.0% 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 Sun Oct 9 2011 at 02:15:41 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1845 !!! WARNING: HIR 75 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: 1.053158 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): -114.2920 -61.72100 ymin,ymax (A): -118.3190 33.79500 zmin,zma (A): -2.307000 51.33500 x,y,z range (A): 52.57100 152.1140 53.64200 scale (grids/A): 1.053158 object centre (A): -88.00650 -42.26200 24.51400 number of atom coordinates read : 1845 total number of charged atoms : 1723 net assigned charge : 6.514015 assigned positive charge : 271.0462 centred at (gu) : 92.93290 29.78226 89.60432 assigned negative charge : -264.5324 centred at (gu) : 92.73965 29.76374 89.71436 start vw surface at 0.1300000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 16076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22792 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.348800 m= 2278 mr = 7960 m= 62 mr = 762 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 9694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 645 ## 51 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10597 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) : 0.7021050 object centre at (A) : -88.00650 -42.26200 24.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2108601E-06 1.4147919E-05 midg,1,midg; midg,igrid,midg 9.8181233E-02 4.0498328E-08 1,midg,midg; igrid,midg,midg -7.2359126E-06 9.4693723E-06 gauss-seidel spectral radius is 0.9950936 estimated iterations to convergence 115 setup time was (sec) 0.5600000 now iterating at: 02:15:42 rms-change max change #iterations 0.8958508 120.3498 at 10iterations 0.2166039 25.02133 at 20iterations 5.2549291E-02 5.028814 at 30iterations 1.2613431E-02 1.305329 at 40iterations 3.0020389E-03 0.3050213 at 50iterations 7.1842404E-04 6.6261292E-02 at 60iterations 1.7302201E-04 1.3931274E-02 at 70iterations 4.4003358E-05 3.3187866E-03 at 80iterations 1.2630499E-05 9.3650818E-04 at 90iterations 4.4754438E-06 3.2043457E-04 at 100iterations 1.8972763E-06 1.2969971E-04 at 110iterations 8.8563792E-07 6.1035156E-05 at 120iterations 4.6370042E-07 3.8146973E-05 at 130iterations 2.9901108E-07 3.0517578E-05 at 140iterations 2.5837210E-07 6.1035156E-05 at 150iterations 2.4378940E-07 6.1035156E-05 at 160iterations 2.4315614E-07 3.0517578E-05 at 170iterations 2.4162500E-07 3.6239624E-05 at 180iterations finished qdiffx linear iterations at : 02:15:51 total time elapsed so far: 9.740000 # loops : 180 mean,max change (kT/e) : 2.4162500E-07 3.6239624E-05 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 02:15:51 9.924u 0.196s 0:10.39 97.3% 0+0k 0+0io 0pf+0w