Mon Oct 10 14:17:20 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 14:17:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 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: 0.5852472 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): 19.61400 80.44300 ymin,ymax (A): -24.70900 33.28700 zmin,zma (A): -33.83600 22.76100 x,y,z range (A): 60.82900 57.99600 56.59700 scale (grids/A): 0.5852472 object centre (A): 50.02850 4.289000 -5.537501 number of atom coordinates read : 2976 total number of charged atoms : 2832 net assigned charge : -1.999984 assigned positive charge : 458.4609 centred at (gu) : 89.68232 89.28947 91.53876 assigned negative charge : -460.4621 centred at (gu) : 89.75405 89.29404 91.59003 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6879 nv = 96 ne = 84 npr = 57164 no. pairs analyzed = 57164 no. exposed pairs = 4167 no. arc points = 29392 no. surface atoms = 1386 nbur = 1590 mkacc time = 0.1000000 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= 343 mr = 3385 m= 6 mr = 47 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 0.2100000 number of dielectric boundary points 3796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2941 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0105571E-10 -2.7279150E-09 midg,1,midg; midg,igrid,midg -4.4655199E-10 -5.3570326E-10 1,midg,midg; igrid,midg,midg 1.5287890E-09 -2.2833448E-09 gauss-seidel spectral radius is 0.9849381 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 14:17:20 rms-change max change #iterations 0.1019561 17.51050 at 10iterations 8.1618996E-03 1.428492 at 20iterations 6.5910612E-04 8.6483002E-02 at 30iterations 5.8020974E-05 8.8825226E-03 at 40iterations 6.7776186E-06 1.0719299E-03 at 50iterations finished qdiffx linear iterations at : 14:17:23 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 6.7776186E-06 1.0719299E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:17:24 3.386u 0.173s 0:04.17 85.1% 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 14:17:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 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: 1.755741 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): 19.61400 80.44300 ymin,ymax (A): -24.70900 33.28700 zmin,zma (A): -33.83600 22.76100 x,y,z range (A): 60.82900 57.99600 56.59700 scale (grids/A): 1.755741 object centre (A): 50.02850 4.289000 -5.537501 number of atom coordinates read : 2976 total number of charged atoms : 2832 net assigned charge : -1.999984 assigned positive charge : 458.4609 centred at (gu) : 89.04646 87.86771 94.61566 assigned negative charge : -460.4621 centred at (gu) : 89.26191 87.88187 94.76963 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 grid for indexing accessible points = 1.400000 m= 24881 mr = 49406 m= 3256 mr = 16745 m= 108 mr = 1843 m= 0 mr = 23 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 34845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 21988 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) : 0.5852472 object centre at (A) : 50.02850 4.289000 -5.537501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1293805E-03 2.3196712E-02 midg,1,midg; midg,igrid,midg 1.7915305E-02 3.2234071E-03 1,midg,midg; igrid,midg,midg -2.4780318E-02 -3.9135609E-02 gauss-seidel spectral radius is 0.9984507 estimated iterations to convergence 202 setup time was (sec) 0.6000000 now iterating at: 14:17:25 rms-change max change #iterations 3.956228 183.2985 at 10iterations 1.750903 65.69318 at 20iterations 0.7756920 27.29355 at 30iterations 0.3452049 11.15600 at 40iterations 0.1538197 5.549838 at 50iterations 6.8396218E-02 2.287643 at 60iterations 3.0463649E-02 1.115964 at 70iterations 1.3543695E-02 0.4532366 at 80iterations 6.0475646E-03 0.1935971 at 90iterations 2.6936850E-03 9.6807957E-02 at 100iterations 1.2014096E-03 4.0287018E-02 at 110iterations 5.3607952E-04 1.8384933E-02 at 120iterations finished qdiffx linear iterations at : 14:17:32 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 5.3607952E-04 1.8384933E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 14:17:33 7.933u 0.190s 0:08.46 95.9% 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 14:17:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 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: 2.633612 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): 19.61400 80.44300 ymin,ymax (A): -24.70900 33.28700 zmin,zma (A): -33.83600 22.76100 x,y,z range (A): 60.82900 57.99600 56.59700 scale (grids/A): 2.633612 object centre (A): 50.02850 4.289000 -5.537501 number of atom coordinates read : 2976 total number of charged atoms : 2832 net assigned charge : -1.999984 assigned positive charge : 458.4609 centred at (gu) : 88.56940 86.80148 96.92320 assigned negative charge : -460.4621 centred at (gu) : 88.89271 86.82278 97.15447 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 172877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 grid for indexing accessible points = 1.400000 m= 82128 mr = 120706 m= 26685 mr = 63855 m= 5493 mr = 20103 m= 547 mr = 3877 m= 13 mr = 308 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 78892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 22651 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) : 1.755741 object centre at (A) : 50.02850 4.289000 -5.537501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1140573 0.2945910 midg,1,midg; midg,igrid,midg 0.4436986 5.1331900E-02 1,midg,midg; igrid,midg,midg -0.3511872 -0.3748627 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 1.160000 now iterating at: 14:17:34 rms-change max change #iterations 9.763122 272.0736 at 10iterations 5.682057 135.4969 at 20iterations 3.261812 62.54028 at 30iterations 1.869983 39.87073 at 40iterations 1.074399 21.12883 at 50iterations 0.6117085 12.10577 at 60iterations 0.3481544 7.600431 at 70iterations 0.1976791 3.842018 at 80iterations 0.1126457 2.080665 at 90iterations 6.3882209E-02 1.264874 at 100iterations 3.6150135E-02 0.6741295 at 110iterations 2.0502456E-02 0.4108706 at 120iterations 1.1607098E-02 0.2426286 at 130iterations 6.5931417E-03 0.1285585 at 140iterations 3.7270605E-03 6.5620422E-02 at 150iterations 2.1130759E-03 4.0145874E-02 at 160iterations 1.1941544E-03 2.3715973E-02 at 170iterations 6.7847106E-04 1.3156891E-02 at 180iterations finished qdiffx linear iterations at : 14:17:45 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 6.7847106E-04 1.3156891E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 14:17:46 12.546u 0.205s 0:13.25 96.1% 0+0k 0+0io 0pf+0w