Tue Oct 11 06:18:52 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 Tue Oct 11 2011 at 06:18:52 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7044065 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): -20.65000 29.88900 ymin,ymax (A): -11.84200 30.68000 zmin,zma (A): -8.494000 38.19300 x,y,z range (A): 50.53900 42.52200 46.68700 scale (grids/A): 0.7044065 object centre (A): 4.619500 9.419001 14.84950 number of atom coordinates read : 2053 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.7910 centred at (gu) : 90.97878 89.81835 91.08334 assigned negative charge : -307.7521 centred at (gu) : 90.90015 89.75356 90.97914 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6944 nv = 96 ne = 84 npr = 40551 no. pairs analyzed = 40551 no. exposed pairs = 2537 no. arc points = 17497 no. surface atoms = 860 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 3950 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1608 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7434569E-10 1.1544818E-07 midg,1,midg; midg,igrid,midg 1.7306597E-08 7.3147213E-08 1,midg,midg; igrid,midg,midg 9.0143253E-09 9.9173597E-08 gauss-seidel spectral radius is 0.9894948 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 06:18:53 rms-change max change #iterations 0.1948570 27.93392 at 10iterations 2.3915714E-02 3.407418 at 20iterations 3.2005394E-03 0.4693222 at 30iterations 5.2273663E-04 7.2746277E-02 at 40iterations 1.2447230E-04 1.6864777E-02 at 50iterations finished qdiffx linear iterations at : 06:18:56 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.2447230E-04 1.6864777E-02 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 06:18:57 4.033u 0.250s 0:04.73 90.4% 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 Tue Oct 11 2011 at 06:18:57 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.113219 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): -20.65000 29.88900 ymin,ymax (A): -11.84200 30.68000 zmin,zma (A): -8.494000 38.19300 x,y,z range (A): 50.53900 42.52200 46.68700 scale (grids/A): 2.113219 object centre (A): 4.619500 9.419001 14.84950 number of atom coordinates read : 2053 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.7910 centred at (gu) : 92.93620 89.45521 93.25025 assigned negative charge : -307.7521 centred at (gu) : 92.70061 89.26080 92.93771 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17497 grid for indexing accessible points = 1.400000 m= 30275 mr = 52690 m= 6065 mr = 23067 m= 585 mr = 4016 m= 14 mr = 286 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 31035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15284 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) : 0.7044065 object centre at (A) : 4.619500 9.419001 14.84950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5763135E-02 4.0003780E-02 midg,1,midg; midg,igrid,midg 2.3593964E-02 2.3824960E-02 1,midg,midg; igrid,midg,midg 4.9915705E-02 4.3185413E-02 gauss-seidel spectral radius is 0.9988226 estimated iterations to convergence 231 setup time was (sec) 1.010000 now iterating at: 06:18:58 rms-change max change #iterations 4.559630 205.9613 at 10iterations 2.245418 75.92264 at 20iterations 1.113955 34.95943 at 30iterations 0.5500384 16.53506 at 40iterations 0.2729566 9.140854 at 50iterations 0.1348609 4.159123 at 60iterations 6.6906169E-02 2.053160 at 70iterations 3.3218473E-02 0.9401708 at 80iterations 1.6586332E-02 0.5397491 at 90iterations 8.3237495E-03 0.2568245 at 100iterations 4.1892454E-03 0.1386414 at 110iterations 2.1638328E-03 6.3486814E-02 at 120iterations finished qdiffx linear iterations at : 06:19:06 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 2.1638328E-03 6.3486814E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 06:19:07 9.552u 0.291s 0:10.32 95.3% 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 Tue Oct 11 2011 at 06:19:07 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.169829 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): -20.65000 29.88900 ymin,ymax (A): -11.84200 30.68000 zmin,zma (A): -8.494000 38.19300 x,y,z range (A): 50.53900 42.52200 46.68700 scale (grids/A): 3.169829 object centre (A): 4.619500 9.419001 14.84950 number of atom coordinates read : 2053 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.7910 centred at (gu) : 94.40440 89.18266 94.87538 assigned negative charge : -307.7521 centred at (gu) : 94.05099 88.89126 94.40659 start vw surface at 0.1500000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 170846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17497 grid for indexing accessible points = 1.400000 m= 93658 mr = 126668 m= 38747 mr = 78042 m= 11211 mr = 31866 m= 2278 mr = 8634 m= 264 mr = 1633 m= 9 mr = 156 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.210000 number of dielectric boundary points 70015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 15384 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) : 2.113219 object centre at (A) : 4.619500 9.419001 14.84950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4989835 0.4005334 midg,1,midg; midg,igrid,midg 0.1780253 0.1576984 1,midg,midg; igrid,midg,midg 0.4495078 0.2700122 gauss-seidel spectral radius is 0.9992962 estimated iterations to convergence 297 setup time was (sec) 2.530000 now iterating at: 06:19:10 rms-change max change #iterations 10.24955 410.0341 at 10iterations 6.046163 117.9095 at 20iterations 3.573914 79.63801 at 30iterations 2.101000 38.93667 at 40iterations 1.235376 22.22646 at 50iterations 0.7264943 14.67694 at 60iterations 0.4258651 8.971053 at 70iterations 0.2497861 4.819552 at 80iterations 0.1462145 2.598351 at 90iterations 8.5956514E-02 1.621674 at 100iterations 5.0515857E-02 0.9209502 at 110iterations 2.9830351E-02 0.5321999 at 120iterations 1.7765053E-02 0.3767776 at 130iterations 1.0760046E-02 0.2179070 at 140iterations 6.7012277E-03 0.1492500 at 150iterations 4.3331403E-03 9.1964722E-02 at 160iterations 2.9712943E-03 6.2393188E-02 at 170iterations 2.1505172E-03 4.8099518E-02 at 180iterations finished qdiffx linear iterations at : 06:19:24 total time elapsed so far: 16.21000 # loops : 180 mean,max change (kT/e) : 2.1505172E-03 4.8099518E-02 energy calculations done at 16.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 06:19:24 16.389u 0.322s 0:17.03 98.0% 0+0k 0+0io 0pf+0w