Sat Oct 8 11:40:23 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 11:40:23 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5819466 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): 13.32100 74.49500 ymin,ymax (A): -1.450000 51.09300 zmin,zma (A): 22.40100 77.85800 x,y,z range (A): 61.17400 52.54300 55.45700 scale (grids/A): 0.5819466 object centre (A): 43.90800 24.82150 50.12950 number of atom coordinates read : 3570 total number of charged atoms : 3448 net assigned charge : -4.471972 assigned positive charge : 549.4266 centred at (gu) : 88.04353 91.10428 89.59396 assigned negative charge : -553.9001 centred at (gu) : 88.11637 90.97328 89.60522 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7933 nv = 96 ne = 84 npr = 72650 no. pairs analyzed = 72650 no. exposed pairs = 4080 no. arc points = 28527 no. surface atoms = 1380 nbur = 2190 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 321 mr = 4584 m= 0 mr = 23 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3500000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2804 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8055979E-10 -1.3298500E-09 midg,1,midg; midg,igrid,midg -3.8650487E-09 3.4322702E-09 1,midg,midg; igrid,midg,midg 1.5920651E-09 -2.0797519E-09 gauss-seidel spectral radius is 0.9847996 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 11:40:24 rms-change max change #iterations 0.1170838 17.89835 at 10iterations 9.4825774E-03 1.494774 at 20iterations 7.5366121E-04 0.1089230 at 30iterations 6.2097155E-05 8.1272125E-03 at 40iterations 5.3945350E-06 7.6866150E-04 at 50iterations finished qdiffx linear iterations at : 11:40:27 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 5.3945350E-06 7.6866150E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 11:40:27 3.196u 0.174s 0:03.70 90.8% 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 Sat Oct 8 2011 at 11:40:27 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 235 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.745840 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): 13.32100 74.49500 ymin,ymax (A): -1.450000 51.09300 zmin,zma (A): 22.40100 77.85800 x,y,z range (A): 61.17400 52.54300 55.45700 scale (grids/A): 1.745840 object centre (A): 43.90800 24.82150 50.12950 number of atom coordinates read : 3570 total number of charged atoms : 3448 net assigned charge : -4.471972 assigned positive charge : 549.4266 centred at (gu) : 84.12930 93.31165 88.78065 assigned negative charge : -553.9001 centred at (gu) : 84.34852 92.91925 88.81499 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28527 grid for indexing accessible points = 1.400000 m= 29621 mr = 62569 m= 3691 mr = 22282 m= 139 mr = 2256 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3663 time to turn everything in is 0.6000000 number of dielectric boundary points 33802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 26742 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) : 0.5819466 object centre at (A) : 43.90800 24.82150 50.12950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3724962E-02 -1.4979326E-02 midg,1,midg; midg,igrid,midg -1.7598918E-02 1.6483255E-02 1,midg,midg; igrid,midg,midg 8.0265023E-04 -2.8221039E-03 gauss-seidel spectral radius is 0.9984676 estimated iterations to convergence 203 setup time was (sec) 0.8800000 now iterating at: 11:40:28 rms-change max change #iterations 4.358544 167.1317 at 10iterations 1.956266 70.48579 at 20iterations 0.8782319 28.77226 at 30iterations 0.3921579 12.33717 at 40iterations 0.1757289 5.321119 at 50iterations 7.8945473E-02 2.468005 at 60iterations 3.5375725E-02 1.103066 at 70iterations 1.5825175E-02 0.4604607 at 80iterations 7.0920712E-03 0.2055035 at 90iterations 3.1918099E-03 9.3833923E-02 at 100iterations 1.4305653E-03 4.3804169E-02 at 110iterations 6.4153067E-04 1.8403292E-02 at 120iterations finished qdiffx linear iterations at : 11:40:36 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 6.4153067E-04 1.8403292E-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) 8.310000 DelPhi exited at 11:40:36 8.316u 0.219s 0:09.00 94.6% 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 11:40:36 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3570 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 235 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.618760 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): 13.32100 74.49500 ymin,ymax (A): -1.450000 51.09300 zmin,zma (A): 22.40100 77.85800 x,y,z range (A): 61.17400 52.54300 55.45700 scale (grids/A): 2.618760 object centre (A): 43.90800 24.82150 50.12950 number of atom coordinates read : 3570 total number of charged atoms : 3448 net assigned charge : -4.471972 assigned positive charge : 549.4266 centred at (gu) : 81.19363 94.96712 88.17075 assigned negative charge : -553.9001 centred at (gu) : 81.52271 94.37871 88.22232 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 203036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28527 grid for indexing accessible points = 1.400000 m= 99936 mr = 151735 m= 32238 mr = 82823 m= 6263 mr = 26227 m= 648 mr = 4654 m= 11 mr = 417 m= 0 mr = 4 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 12677 time to turn everything in is 1.450000 number of dielectric boundary points 76272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 27577 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) : 1.745840 object centre at (A) : 43.90800 24.82150 50.12950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1946855 -0.2172475 midg,1,midg; midg,igrid,midg -0.1990994 0.1402833 1,midg,midg; igrid,midg,midg -1.3688807E-03 5.4650526E-02 gauss-seidel spectral radius is 0.9992225 estimated iterations to convergence 283 setup time was (sec) 1.770000 now iterating at: 11:40:38 rms-change max change #iterations 10.56775 276.2259 at 10iterations 6.069555 136.5413 at 20iterations 3.467506 67.22201 at 30iterations 1.971756 36.88887 at 40iterations 1.122834 19.21754 at 50iterations 0.6377225 12.10469 at 60iterations 0.3612656 6.026237 at 70iterations 0.2050577 3.759413 at 80iterations 0.1162758 1.910946 at 90iterations 6.5850742E-02 1.231585 at 100iterations 3.7362393E-02 0.6528530 at 110iterations 2.1145025E-02 0.3670632 at 120iterations 1.1993014E-02 0.2063718 at 130iterations 6.7910855E-03 0.1173096 at 140iterations 3.8427273E-03 6.9998503E-02 at 150iterations 2.1807125E-03 3.5449982E-02 at 160iterations 1.2345666E-03 2.1536350E-02 at 170iterations 6.9810572E-04 1.1878967E-02 at 180iterations finished qdiffx linear iterations at : 11:40:49 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 6.9810572E-04 1.1878967E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 11:40:49 12.325u 0.226s 0:12.93 96.9% 0+0k 0+0io 0pf+0w