Sat Oct 8 20:40:46 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 Sat Oct 8 2011 at 20:40:46 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 607 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6203712 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): -32.33500 17.55100 ymin,ymax (A): -24.09900 22.67500 zmin,zma (A): -12.40000 44.98500 x,y,z range (A): 49.88600 46.77400 57.38500 scale (grids/A): 0.6203712 object centre (A): -7.391999 -0.7119999 16.29250 number of atom coordinates read : 2587 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 88.72695 89.34519 89.66428 assigned negative charge : -390.4956 centred at (gu) : 88.61952 89.37735 89.55936 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6618 nv = 96 ne = 84 npr = 53182 no. pairs analyzed = 53182 no. exposed pairs = 2998 no. arc points = 21895 no. surface atoms = 1010 nbur = 1577 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3745 m= 0 mr = 44 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.3100000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6629992E-09 1.0007619E-08 midg,1,midg; midg,igrid,midg 6.8527011E-09 1.4088625E-09 1,midg,midg; igrid,midg,midg -4.8171915E-09 8.2805345E-09 gauss-seidel spectral radius is 0.9865407 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 20:40:47 rms-change max change #iterations 0.1282876 18.33482 at 10iterations 1.1600421E-02 1.673248 at 20iterations 1.0839731E-03 0.1585283 at 30iterations 9.8859164E-05 1.5689850E-02 at 40iterations 9.2112596E-06 1.4724731E-03 at 50iterations finished qdiffx linear iterations at : 20:40:49 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 9.2112596E-06 1.4724731E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 20:40:49 3.145u 0.134s 0:03.57 91.5% 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 Sat Oct 8 2011 at 20:40:50 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.861113 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): -32.33500 17.55100 ymin,ymax (A): -24.09900 22.67500 zmin,zma (A): -12.40000 44.98500 x,y,z range (A): 49.88600 46.77400 57.38500 scale (grids/A): 1.861113 object centre (A): -7.391999 -0.7119999 16.29250 number of atom coordinates read : 2587 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 86.18019 88.03526 88.99250 assigned negative charge : -390.4956 centred at (gu) : 85.85821 88.13180 88.67770 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21895 grid for indexing accessible points = 1.400000 m= 25588 mr = 50230 m= 3690 mr = 19128 m= 201 mr = 2350 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5082 time to turn everything in is 0.5000000 number of dielectric boundary points 29405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19343 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) : 0.6203712 object centre at (A) : -7.391999 -0.7119999 16.29250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5015088E-02 2.1946600E-02 midg,1,midg; midg,igrid,midg 8.7321717E-03 5.3383890E-03 1,midg,midg; igrid,midg,midg -4.3484177E-03 4.3428868E-02 gauss-seidel spectral radius is 0.9985700 estimated iterations to convergence 210 setup time was (sec) 0.7600000 now iterating at: 20:40:50 rms-change max change #iterations 4.044546 163.1514 at 10iterations 1.856219 63.21050 at 20iterations 0.8538114 27.91932 at 30iterations 0.3927077 12.70937 at 40iterations 0.1810507 6.205206 at 50iterations 8.3399288E-02 2.691406 at 60iterations 3.8341679E-02 1.233842 at 70iterations 1.7629877E-02 0.5766029 at 80iterations 8.1016710E-03 0.2614174 at 90iterations 3.7410529E-03 0.1137981 at 100iterations 1.7169655E-03 5.9902191E-02 at 110iterations 7.9418841E-04 2.6397705E-02 at 120iterations finished qdiffx linear iterations at : 20:40:56 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 7.9418841E-04 2.6397705E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 20:40:57 6.943u 0.167s 0:07.45 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 Sat Oct 8 2011 at 20:40:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 607 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.791670 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): -32.33500 17.55100 ymin,ymax (A): -24.09900 22.67500 zmin,zma (A): -12.40000 44.98500 x,y,z range (A): 49.88600 46.77400 57.38500 scale (grids/A): 2.791670 object centre (A): -7.391999 -0.7119999 16.29250 number of atom coordinates read : 2587 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 84.27012 87.05280 88.48872 assigned negative charge : -390.4956 centred at (gu) : 83.78739 87.19766 88.01654 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 165823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21895 grid for indexing accessible points = 1.400000 m= 84036 mr = 121380 m= 29439 mr = 69768 m= 6578 mr = 23677 m= 903 mr = 4991 m= 55 mr = 618 m= 0 mr = 23 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 16955 time to turn everything in is 1.210000 number of dielectric boundary points 66377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19726 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) : 1.861113 object centre at (A) : -7.391999 -0.7119999 16.29250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1039472 0.2641501 midg,1,midg; midg,igrid,midg 0.1003008 5.7415720E-02 1,midg,midg; igrid,midg,midg -3.8199790E-02 0.5939038 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 1.500000 now iterating at: 20:40:59 rms-change max change #iterations 9.503380 323.6351 at 10iterations 5.440238 113.0447 at 20iterations 3.105948 77.72960 at 30iterations 1.771150 33.81659 at 40iterations 1.009760 23.68453 at 50iterations 0.5742525 12.84173 at 60iterations 0.3271929 6.487080 at 70iterations 0.1856790 3.724360 at 80iterations 0.1058350 2.044568 at 90iterations 6.0041767E-02 1.171175 at 100iterations 3.4216143E-02 0.6752744 at 110iterations 1.9456755E-02 0.3682318 at 120iterations 1.1043010E-02 0.2218189 at 130iterations 6.2863198E-03 0.1152000 at 140iterations 3.5760333E-03 6.5492630E-02 at 150iterations 2.0333233E-03 3.5492420E-02 at 160iterations 1.1559024E-03 2.0170212E-02 at 170iterations 6.5673079E-04 1.3329506E-02 at 180iterations finished qdiffx linear iterations at : 20:41:08 total time elapsed so far: 11.07000 # loops : 180 mean,max change (kT/e) : 6.5673079E-04 1.3329506E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 20:41:09 11.248u 0.176s 0:11.70 97.5% 0+0k 0+0io 0pf+0w