Mon Oct 10 14:20:08 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 14:20:08 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5912050 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): -10.31400 38.27300 ymin,ymax (A): -16.76000 39.44200 zmin,zma (A): -19.03500 41.18100 x,y,z range (A): 48.58700 56.20200 60.21600 scale (grids/A): 0.5912050 object centre (A): 13.97950 11.34100 11.07300 number of atom coordinates read : 2577 total number of charged atoms : 2420 net assigned charge : -0.9999908 assigned positive charge : 383.5070 centred at (gu) : 90.53764 89.79018 88.83801 assigned negative charge : -384.5074 centred at (gu) : 90.35583 89.89620 88.98500 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5929 nv = 96 ne = 84 npr = 52183 no. pairs analyzed = 52183 no. exposed pairs = 3421 no. arc points = 23936 no. surface atoms = 1155 nbur = 1422 mkacc time = 0.1600000 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= 267 mr = 3032 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6878190E-09 -3.4340963E-09 midg,1,midg; midg,igrid,midg 2.5954121E-09 -3.1814877E-09 1,midg,midg; igrid,midg,midg -4.8420716E-09 5.0827484E-09 gauss-seidel spectral radius is 0.9851978 estimated iterations to convergence 67 setup time was (sec) 0.6800000 now iterating at: 14:20:09 rms-change max change #iterations 0.1007656 17.83031 at 10iterations 8.2017817E-03 1.333902 at 20iterations 6.6885387E-04 9.9445343E-02 at 30iterations 5.4981636E-05 8.6746216E-03 at 40iterations 4.4822477E-06 7.8535080E-04 at 50iterations finished qdiffx linear iterations at : 14:20:12 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 4.4822477E-06 7.8535080E-04 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 14:20:13 4.289u 0.219s 0:04.91 91.4% 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 14:20:13 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.773615 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): -10.31400 38.27300 ymin,ymax (A): -16.76000 39.44200 zmin,zma (A): -19.03500 41.18100 x,y,z range (A): 48.58700 56.20200 60.21600 scale (grids/A): 1.773615 object centre (A): 13.97950 11.34100 11.07300 number of atom coordinates read : 2577 total number of charged atoms : 2420 net assigned charge : -0.9999908 assigned positive charge : 383.5070 centred at (gu) : 91.61243 89.37011 86.51340 assigned negative charge : -384.5074 centred at (gu) : 91.06716 89.68829 86.95455 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23936 grid for indexing accessible points = 1.400000 m= 20907 mr = 43757 m= 2518 mr = 14383 m= 113 mr = 1201 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 29226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18823 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) : 0.5912050 object centre at (A) : 13.97950 11.34100 11.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9401707E-03 2.0979086E-03 midg,1,midg; midg,igrid,midg -5.5743675E-03 -5.8624474E-03 1,midg,midg; igrid,midg,midg -2.1724716E-02 3.4520940E-03 gauss-seidel spectral radius is 0.9984294 estimated iterations to convergence 200 setup time was (sec) 0.9700000 now iterating at: 14:20:14 rms-change max change #iterations 3.683343 188.8448 at 10iterations 1.614727 73.23219 at 20iterations 0.7155482 24.44377 at 30iterations 0.3176187 12.04860 at 40iterations 0.1402192 5.164459 at 50iterations 6.2148787E-02 2.442764 at 60iterations 2.7630605E-02 0.9855499 at 70iterations 1.2215379E-02 0.4449577 at 80iterations 5.4093376E-03 0.1981506 at 90iterations 2.3987340E-03 9.2126846E-02 at 100iterations 1.0612708E-03 3.3262491E-02 at 110iterations 4.7111191E-04 1.8372536E-02 at 120iterations finished qdiffx linear iterations at : 14:20:23 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 4.7111191E-04 1.8372536E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 14:20:23 9.673u 0.287s 0:10.34 96.2% 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 14:20:23 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 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: 2.660423 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): -10.31400 38.27300 ymin,ymax (A): -16.76000 39.44200 zmin,zma (A): -19.03500 41.18100 x,y,z range (A): 48.58700 56.20200 60.21600 scale (grids/A): 2.660423 object centre (A): 13.97950 11.34100 11.07300 number of atom coordinates read : 2577 total number of charged atoms : 2420 net assigned charge : -0.9999908 assigned positive charge : 383.5070 centred at (gu) : 92.41872 89.05496 84.76997 assigned negative charge : -384.5074 centred at (gu) : 91.60068 89.53222 85.43170 start vw surface at 0.1900000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 150873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23936 grid for indexing accessible points = 1.400000 m= 70469 mr = 106960 m= 21809 mr = 55800 m= 4002 mr = 16193 m= 393 mr = 2578 m= 19 mr = 203 m= 0 mr = 7 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 65824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19350 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) : 1.773615 object centre at (A) : 13.97950 11.34100 11.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6204116E-02 6.7561477E-02 midg,1,midg; midg,igrid,midg -0.2325976 -8.0867387E-02 1,midg,midg; igrid,midg,midg -0.2615529 -1.1358501E-02 gauss-seidel spectral radius is 0.9992055 estimated iterations to convergence 280 setup time was (sec) 1.910000 now iterating at: 14:20:25 rms-change max change #iterations 9.021620 328.2972 at 10iterations 5.219275 144.4872 at 20iterations 2.988141 70.89191 at 30iterations 1.702321 39.27727 at 40iterations 0.9671721 21.10848 at 50iterations 0.5486526 11.58888 at 60iterations 0.3106570 6.558941 at 70iterations 0.1755042 3.327015 at 80iterations 9.9357367E-02 1.902727 at 90iterations 5.5996511E-02 1.181698 at 100iterations 3.1668331E-02 0.6755247 at 110iterations 1.7780254E-02 0.3803291 at 120iterations 1.0049606E-02 0.2017126 at 130iterations 5.6518950E-03 0.1201024 at 140iterations 3.1844196E-03 6.5738678E-02 at 150iterations 1.7904436E-03 3.7090302E-02 at 160iterations 1.0074775E-03 1.9832611E-02 at 170iterations 5.6730007E-04 1.1862755E-02 at 180iterations finished qdiffx linear iterations at : 14:20:38 total time elapsed so far: 14.79000 # loops : 180 mean,max change (kT/e) : 5.6730007E-04 1.1862755E-02 energy calculations done at 14.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.02000 DelPhi exited at 14:20:39 15.020u 0.298s 0:15.66 97.7% 0+0k 0+0io 0pf+0w