Wed Dec 21 14:20:59 PST 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 Wed Dec 21 2011 at 14:20:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1861 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 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: 0.6099650 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): -23.86100 34.50300 ymin,ymax (A): -18.51500 20.62200 zmin,zma (A): -3.312000 38.67000 x,y,z range (A): 58.36400 39.13700 41.98200 scale (grids/A): 0.6099650 object centre (A): 5.321001 1.053500 17.67900 number of atom coordinates read : 1861 total number of charged atoms : 1729 net assigned charge : -5.732985 assigned positive charge : 270.2772 centred at (gu) : 89.78435 90.17545 90.53287 assigned negative charge : -276.0103 centred at (gu) : 89.84184 90.26100 90.60748 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4757 nv = 96 ne = 84 npr = 38379 no. pairs analyzed = 38379 no. exposed pairs = 2478 no. arc points = 16875 no. surface atoms = 838 nbur = 1023 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 265 mr = 2549 m= 0 mr = 22 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1656 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 5654 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9119771E-10 -6.7619168E-09 midg,1,midg; midg,igrid,midg -3.7293604E-10 -6.6533512E-09 1,midg,midg; igrid,midg,midg -1.4113607E-09 -5.1457003E-09 gauss-seidel spectral radius is 0.9860243 estimated iterations to convergence 69 setup time was (sec) 0.5300000 now iterating at: 14:21:00 rms-change max change #iterations 9.6883051E-02 16.46556 at 10iterations 8.6183771E-03 1.494137 at 20iterations 7.4046670E-04 0.1295471 at 30iterations 6.5434389E-05 1.1930466E-02 at 40iterations 5.8274841E-06 9.9658966E-04 at 50iterations finished qdiffx linear iterations at : 14:21:03 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 5.8274841E-06 9.9658966E-04 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 14:21:04 3.972u 0.258s 0:04.86 86.8% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:04 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1861 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 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: 1.829895 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): -23.86100 34.50300 ymin,ymax (A): -18.51500 20.62200 zmin,zma (A): -3.312000 38.67000 x,y,z range (A): 58.36400 39.13700 41.98200 scale (grids/A): 1.829895 object centre (A): 5.321001 1.053500 17.67900 number of atom coordinates read : 1861 total number of charged atoms : 1729 net assigned charge : -5.732985 assigned positive charge : 270.2772 centred at (gu) : 89.35327 90.52664 91.59887 assigned negative charge : -276.0103 centred at (gu) : 89.52576 90.78329 91.82262 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 51019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16875 grid for indexing accessible points = 1.400000 m= 18602 mr = 34566 m= 2829 mr = 13836 m= 115 mr = 1775 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 331 time to turn everything in is 0.4900000 number of dielectric boundary points 22367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13574 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) : 0.6099650 object centre at (A) : 5.321001 1.053500 17.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1688525E-03 -1.1301326E-02 midg,1,midg; midg,igrid,midg -1.2237767E-03 -6.1734011E-03 1,midg,midg; igrid,midg,midg 1.4421774E-02 -1.2331052E-02 gauss-seidel spectral radius is 0.9984388 estimated iterations to convergence 201 setup time was (sec) 0.7800000 now iterating at: 14:21:05 rms-change max change #iterations 3.215799 174.2426 at 10iterations 1.428959 54.65160 at 20iterations 0.6351847 25.70395 at 30iterations 0.2816277 10.85604 at 40iterations 0.1251861 4.653221 at 50iterations 5.5584092E-02 2.243782 at 60iterations 2.4558026E-02 0.9449303 at 70iterations 1.0939889E-02 0.4447422 at 80iterations 4.8582205E-03 0.1982384 at 90iterations 2.1576413E-03 8.9407921E-02 at 100iterations 9.5963804E-04 4.2101383E-02 at 110iterations 4.2616457E-04 1.6891479E-02 at 120iterations finished qdiffx linear iterations at : 14:21:15 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 4.2616457E-04 1.6891479E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 14:21:16 10.874u 0.394s 0:11.78 95.5% 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 Wed Dec 21 2011 at 14:21:16 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1861 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 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: 2.744843 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): -23.86100 34.50300 ymin,ymax (A): -18.51500 20.62200 zmin,zma (A): -3.312000 38.67000 x,y,z range (A): 58.36400 39.13700 41.98200 scale (grids/A): 2.744843 object centre (A): 5.321001 1.053500 17.67900 number of atom coordinates read : 1861 total number of charged atoms : 1729 net assigned charge : -5.732985 assigned positive charge : 270.2772 centred at (gu) : 89.03001 90.78985 92.39835 assigned negative charge : -276.0103 centred at (gu) : 89.28878 91.17486 92.73403 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 117827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16875 grid for indexing accessible points = 1.400000 m= 59940 mr = 83882 m= 21889 mr = 49098 m= 5074 mr = 17773 m= 482 mr = 3855 m= 13 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 1.220000 number of dielectric boundary points 50355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 13831 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) : 1.829895 object centre at (A) : 5.321001 1.053500 17.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0155307E-02 -0.1006974 midg,1,midg; midg,igrid,midg -7.4057239E-03 -4.1372441E-02 1,midg,midg; igrid,midg,midg 0.2149548 -0.1605473 gauss-seidel spectral radius is 0.9991882 estimated iterations to convergence 277 setup time was (sec) 1.640000 now iterating at: 14:21:18 rms-change max change #iterations 7.811338 360.1831 at 10iterations 4.458313 126.8021 at 20iterations 2.522598 70.62187 at 30iterations 1.420817 31.58622 at 40iterations 0.7991372 22.08945 at 50iterations 0.4480804 11.12110 at 60iterations 0.2504739 5.459953 at 70iterations 0.1406516 3.188900 at 80iterations 7.8574732E-02 1.680412 at 90iterations 4.4053867E-02 1.014535 at 100iterations 2.4618335E-02 0.5513763 at 110iterations 1.3756393E-02 0.2886610 at 120iterations 7.6832329E-03 0.1749420 at 130iterations 4.3057953E-03 9.2433929E-02 at 140iterations 2.4012481E-03 4.9009323E-02 at 150iterations 1.3409206E-03 3.1522751E-02 at 160iterations 7.4979884E-04 1.7087936E-02 at 170iterations 4.1915392E-04 1.0282636E-02 at 180iterations finished qdiffx linear iterations at : 14:21:34 total time elapsed so far: 17.13000 # loops : 180 mean,max change (kT/e) : 4.1915392E-04 1.0282636E-02 energy calculations done at 17.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.32000 DelPhi exited at 14:21:36 17.326u 0.572s 0:20.19 88.6% 0+0k 0+0io 0pf+0w