Mon Oct 10 17:03:33 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 17:03:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3443 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: MG6 686 has a net charge of 1.4000 !!! WARNING: ZN6 688 has a net charge of 1.4000 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: 0.5876527 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): -50.23100 7.168000 ymin,ymax (A): -22.56100 38.01900 zmin,zma (A): -64.76900 -9.707999 x,y,z range (A): 57.39900 60.58000 55.06100 scale (grids/A): 0.5876527 object centre (A): -21.53150 7.728998 -37.23850 number of atom coordinates read : 3443 total number of charged atoms : 3295 net assigned charge : 6.200036 assigned positive charge : 525.7240 centred at (gu) : 88.72879 88.90312 90.63901 assigned negative charge : -519.5259 centred at (gu) : 88.75195 89.02659 90.49570 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7696 nv = 96 ne = 84 npr = 70163 no. pairs analyzed = 70163 no. exposed pairs = 4496 no. arc points = 31219 no. surface atoms = 1475 nbur = 1968 mkacc time = 0.1200000 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= 399 mr = 3990 m= 0 mr = 36 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3087 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6883211E-09 7.3266717E-09 midg,1,midg; midg,igrid,midg 7.3359860E-09 -1.8865076E-09 1,midg,midg; igrid,midg,midg 3.2487395E-09 6.8959799E-10 gauss-seidel spectral radius is 0.9850890 estimated iterations to convergence 67 setup time was (sec) 0.4700000 now iterating at: 17:03:33 rms-change max change #iterations 0.1161755 16.93020 at 10iterations 9.6450672E-03 1.349823 at 20iterations 1.1009711E-03 0.1485691 at 30iterations 2.6060495E-04 3.6869049E-02 at 40iterations 8.2544429E-05 1.1635780E-02 at 50iterations finished qdiffx linear iterations at : 17:03:37 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 8.2544429E-05 1.1635780E-02 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 17:03:39 3.809u 0.233s 0:05.96 67.6% 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 Mon Oct 10 2011 at 17:03:39 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3443 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: MG6 686 has a net charge of 1.4000 !!! WARNING: ZN6 688 has a net charge of 1.4000 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: 1.762958 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): -50.23100 7.168000 ymin,ymax (A): -22.56100 38.01900 zmin,zma (A): -64.76900 -9.707999 x,y,z range (A): 57.39900 60.58000 55.06100 scale (grids/A): 1.762958 object centre (A): -21.53150 7.728998 -37.23850 number of atom coordinates read : 3443 total number of charged atoms : 3295 net assigned charge : 6.200036 assigned positive charge : 525.7240 centred at (gu) : 86.18549 86.70856 91.91609 assigned negative charge : -519.5259 centred at (gu) : 86.25545 87.07948 91.48662 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31219 grid for indexing accessible points = 1.400000 m= 28845 mr = 57215 m= 4003 mr = 19993 m= 155 mr = 2176 m= 0 mr = 39 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 0.4400000 number of dielectric boundary points 37851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 25658 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) : 0.5876527 object centre at (A) : -21.53150 7.728998 -37.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6722621E-02 3.1936646E-02 midg,1,midg; midg,igrid,midg 3.3122338E-02 -1.5502945E-02 1,midg,midg; igrid,midg,midg 2.2746408E-02 2.8667368E-03 gauss-seidel spectral radius is 0.9985014 estimated iterations to convergence 205 setup time was (sec) 0.7300000 now iterating at: 17:03:40 rms-change max change #iterations 4.310803 179.1394 at 10iterations 1.940490 71.48426 at 20iterations 0.8792281 28.49791 at 30iterations 0.3951328 12.27861 at 40iterations 0.1789649 5.516264 at 50iterations 8.0796905E-02 2.475142 at 60iterations 3.6675002E-02 1.080044 at 70iterations 1.6640343E-02 0.5431273 at 80iterations 7.5760032E-03 0.2401581 at 90iterations 3.4719245E-03 0.1114788 at 100iterations 1.6221153E-03 5.3703308E-02 at 110iterations 7.7809201E-04 2.5691032E-02 at 120iterations finished qdiffx linear iterations at : 17:03:49 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 7.7809201E-04 2.5691032E-02 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 17:03:49 8.743u 0.301s 0:10.61 85.2% 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 17:03:49 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3443 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: MG6 686 has a net charge of 1.4000 !!! WARNING: ZN6 688 has a net charge of 1.4000 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: 2.644437 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): -50.23100 7.168000 ymin,ymax (A): -22.56100 38.01900 zmin,zma (A): -64.76900 -9.707999 x,y,z range (A): 57.39900 60.58000 55.06100 scale (grids/A): 2.644437 object centre (A): -21.53150 7.728998 -37.23850 number of atom coordinates read : 3443 total number of charged atoms : 3295 net assigned charge : 6.200036 assigned positive charge : 525.7240 centred at (gu) : 84.27785 85.06229 92.87377 assigned negative charge : -519.5259 centred at (gu) : 84.38316 85.61929 92.22982 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 195312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31219 grid for indexing accessible points = 1.400000 m= 94373 mr = 139833 m= 32306 mr = 74429 m= 6753 mr = 24717 m= 710 mr = 4696 m= 27 mr = 399 m= 0 mr = 8 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 758 time to turn everything in is 1.070000 number of dielectric boundary points 85399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 26354 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) : 1.762958 object centre at (A) : -21.53150 7.728998 -37.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2202228 0.3772984 midg,1,midg; midg,igrid,midg 0.4270817 -0.1351138 1,midg,midg; igrid,midg,midg 0.2235978 9.3265086E-02 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.340000 now iterating at: 17:03:51 rms-change max change #iterations 10.69088 286.1692 at 10iterations 6.279321 146.4820 at 20iterations 3.676705 91.84279 at 30iterations 2.136213 48.94071 at 40iterations 1.238338 28.37640 at 50iterations 0.7161655 16.32041 at 60iterations 0.4123224 8.544018 at 70iterations 0.2371197 4.657969 at 80iterations 0.1363100 2.976761 at 90iterations 7.8294195E-02 1.462812 at 100iterations 4.4946581E-02 0.8905258 at 110iterations 2.5785511E-02 0.4943008 at 120iterations 1.4749302E-02 0.2728634 at 130iterations 8.4702978E-03 0.1593533 at 140iterations 4.8575234E-03 9.4245911E-02 at 150iterations 2.8039864E-03 4.8951566E-02 at 160iterations 1.6241487E-03 2.8247833E-02 at 170iterations 9.5194398E-04 1.9823074E-02 at 180iterations finished qdiffx linear iterations at : 17:04:08 total time elapsed so far: 14.73000 # loops : 180 mean,max change (kT/e) : 9.5194398E-04 1.9823074E-02 energy calculations done at 14.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.86000 DelPhi exited at 17:04:09 14.861u 0.288s 0:19.64 77.0% 0+0k 0+0io 0pf+0w