Mon Oct 10 17:02:41 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 Mon Oct 10 2011 at 17:02:41 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 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: 0.7335820 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): 32.74900 81.27800 ymin,ymax (A): 15.82000 54.98300 zmin,zma (A): 26.02000 61.02900 x,y,z range (A): 48.52900 39.16300 35.00900 scale (grids/A): 0.7335820 object centre (A): 57.01350 35.40150 43.52450 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 89.82061 89.03255 88.96487 assigned negative charge : -192.8082 centred at (gu) : 89.71774 89.11685 88.90711 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4716 nv = 96 ne = 84 npr = 27802 no. pairs analyzed = 27802 no. exposed pairs = 1662 no. arc points = 12141 no. surface atoms = 562 nbur = 799 mkacc time = 6.0000010E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 2458 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1109 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 5134 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5765604E-07 2.2825590E-07 midg,1,midg; midg,igrid,midg 3.4609474E-07 1.6775572E-07 1,midg,midg; igrid,midg,midg 1.9526382E-07 2.8959636E-07 gauss-seidel spectral radius is 0.9902344 estimated iterations to convergence 82 setup time was (sec) 0.4000000 now iterating at: 17:02:42 rms-change max change #iterations 0.1851256 36.37849 at 10iterations 2.3825970E-02 3.586296 at 20iterations 3.1732882E-03 0.5510092 at 30iterations 4.0686995E-04 6.8469763E-02 at 40iterations 5.3621989E-05 7.7018738E-03 at 50iterations finished qdiffx linear iterations at : 17:02:44 total time elapsed so far: 2.810000 # loops : 50 mean,max change (kT/e) : 5.3621989E-05 7.7018738E-03 energy calculations done at 2.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 17:02:45 2.991u 0.152s 0:03.65 86.0% 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 Mon Oct 10 2011 at 17:02:45 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 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: 2.200746 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): 32.74900 81.27800 ymin,ymax (A): 15.82000 54.98300 zmin,zma (A): 26.02000 61.02900 x,y,z range (A): 48.52900 39.16300 35.00900 scale (grids/A): 2.200746 object centre (A): 57.01350 35.40150 43.52450 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 89.46187 87.09798 86.89473 assigned negative charge : -192.8082 centred at (gu) : 89.15326 87.35067 86.72158 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 49389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12141 grid for indexing accessible points = 1.400000 m= 17274 mr = 32556 m= 3207 mr = 12319 m= 302 mr = 2044 m= 9 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 23118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9854 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) : 0.7335820 object centre at (A) : 57.01350 35.40150 43.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9400652E-02 3.3048935E-02 midg,1,midg; midg,igrid,midg 7.4695587E-02 2.3161292E-02 1,midg,midg; igrid,midg,midg 0.1157002 0.1128925 gauss-seidel spectral radius is 0.9988275 estimated iterations to convergence 231 setup time was (sec) 0.6400000 now iterating at: 17:02:46 rms-change max change #iterations 3.809413 186.4941 at 10iterations 1.888441 84.59228 at 20iterations 0.9276116 35.34266 at 30iterations 0.4578680 15.63674 at 40iterations 0.2259936 8.553121 at 50iterations 0.1119056 4.006528 at 60iterations 5.5274896E-02 2.009880 at 70iterations 2.7299639E-02 1.062911 at 80iterations 1.3521109E-02 0.4768696 at 90iterations 6.6749007E-03 0.2431641 at 100iterations 3.2961750E-03 0.1215057 at 110iterations 1.6297498E-03 6.0131073E-02 at 120iterations finished qdiffx linear iterations at : 17:02:52 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 1.6297498E-03 6.0131073E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 17:02:53 7.130u 0.171s 0:07.65 95.4% 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 17:02:53 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 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: 3.301119 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): 32.74900 81.27800 ymin,ymax (A): 15.82000 54.98300 zmin,zma (A): 26.02000 61.02900 x,y,z range (A): 48.52900 39.16300 35.00900 scale (grids/A): 3.301119 object centre (A): 57.01350 35.40150 43.52450 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 89.19292 85.64697 85.34218 assigned negative charge : -192.8082 centred at (gu) : 88.72991 86.02607 85.08239 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 113641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12141 grid for indexing accessible points = 1.400000 m= 55013 mr = 78876 m= 21056 mr = 44066 m= 6042 mr = 16587 m= 1252 mr = 4532 m= 133 mr = 897 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 52098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 9904 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) : 2.200746 object centre at (A) : 57.01350 35.40150 43.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2636591 0.1996737 midg,1,midg; midg,igrid,midg 0.6019028 0.1249407 1,midg,midg; igrid,midg,midg 1.007295 0.9390184 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 1.400000 now iterating at: 17:02:54 rms-change max change #iterations 8.462471 274.5559 at 10iterations 4.974005 181.0348 at 20iterations 2.907936 75.74571 at 30iterations 1.697974 40.74245 at 40iterations 0.9905183 21.56439 at 50iterations 0.5753435 12.63004 at 60iterations 0.3348980 7.355692 at 70iterations 0.1944808 3.905487 at 80iterations 0.1129092 2.465771 at 90iterations 6.5684415E-02 1.388084 at 100iterations 3.8054019E-02 0.8330898 at 110iterations 2.2043334E-02 0.4511762 at 120iterations 1.2844687E-02 0.2681507 at 130iterations 7.4327663E-03 0.1384481 at 140iterations 4.3083928E-03 9.0077400E-02 at 150iterations 2.4929694E-03 5.3478241E-02 at 160iterations 1.4475198E-03 3.2421350E-02 at 170iterations 8.3994033E-04 1.6280174E-02 at 180iterations finished qdiffx linear iterations at : 17:03:03 total time elapsed so far: 10.43000 # loops : 180 mean,max change (kT/e) : 8.3994033E-04 1.6280174E-02 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 17:03:04 10.618u 0.178s 0:11.82 91.2% 0+0k 0+0io 0pf+0w