Sat Oct 8 14:20:50 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 Sat Oct 8 2011 at 14:20:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3028 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6150338 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): -35.03700 14.15100 ymin,ymax (A): -15.46600 35.64400 zmin,zma (A): -45.32500 12.55800 x,y,z range (A): 49.18800 51.11000 57.88300 scale (grids/A): 0.6150338 object centre (A): -10.44300 10.08900 -16.38350 number of atom coordinates read : 3028 total number of charged atoms : 2881 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4966 centred at (gu) : 88.23733 89.04534 87.02441 assigned negative charge : -453.4973 centred at (gu) : 88.18777 89.01128 87.11860 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7471 nv = 96 ne = 84 npr = 63224 no. pairs analyzed = 63224 no. exposed pairs = 3515 no. arc points = 24106 no. surface atoms = 1192 nbur = 1836 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 4304 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2391 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2004662E-08 -3.3116274E-09 midg,1,midg; midg,igrid,midg -2.9533769E-09 1.7184065E-09 1,midg,midg; igrid,midg,midg -5.1057447E-09 2.1207198E-09 gauss-seidel spectral radius is 0.9863401 estimated iterations to convergence 70 setup time was (sec) 0.5900000 now iterating at: 14:20:51 rms-change max change #iterations 0.1321662 19.32692 at 10iterations 1.2407733E-02 1.727578 at 20iterations 1.2594238E-03 0.1833954 at 30iterations 1.6332389E-04 2.4493217E-02 at 40iterations 3.0165213E-05 4.2839050E-03 at 50iterations finished qdiffx linear iterations at : 14:20:55 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 3.0165213E-05 4.2839050E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 14:20:55 4.276u 0.266s 0:04.86 93.2% 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 Sat Oct 8 2011 at 14:20:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3028 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.845101 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): -35.03700 14.15100 ymin,ymax (A): -15.46600 35.64400 zmin,zma (A): -45.32500 12.55800 x,y,z range (A): 49.18800 51.11000 57.88300 scale (grids/A): 1.845101 object centre (A): -10.44300 10.08900 -16.38350 number of atom coordinates read : 3028 total number of charged atoms : 2881 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4966 centred at (gu) : 84.71161 87.13531 81.07269 assigned negative charge : -453.4973 centred at (gu) : 84.56265 87.03364 81.35540 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24106 grid for indexing accessible points = 1.400000 m= 28681 mr = 59210 m= 3766 mr = 21243 m= 146 mr = 2151 m= 0 mr = 29 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 32155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22587 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) : 0.6150338 object centre at (A) : -10.44300 10.08900 -16.38350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0986458E-02 -2.9139945E-02 midg,1,midg; midg,igrid,midg -8.1299042E-04 9.2785135E-03 1,midg,midg; igrid,midg,midg -9.8262997E-03 2.3222954E-03 gauss-seidel spectral radius is 0.9985775 estimated iterations to convergence 210 setup time was (sec) 0.9300000 now iterating at: 14:20:56 rms-change max change #iterations 4.373353 172.7538 at 10iterations 2.010223 68.88017 at 20iterations 0.9352086 30.01335 at 30iterations 0.4298896 13.94486 at 40iterations 0.1985468 5.940990 at 50iterations 9.1910012E-02 2.771797 at 60iterations 4.2464081E-02 1.305461 at 70iterations 1.9600606E-02 0.6207767 at 80iterations 9.0485131E-03 0.2645004 at 90iterations 4.1868752E-03 0.1253099 at 100iterations 1.9510244E-03 6.1130524E-02 at 110iterations 8.9867995E-04 2.7681351E-02 at 120iterations finished qdiffx linear iterations at : 14:21:05 total time elapsed so far: 9.980000 # loops : 120 mean,max change (kT/e) : 8.9867995E-04 2.7681351E-02 energy calculations done at 9.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.16000 DelPhi exited at 14:21:06 10.160u 0.298s 0:10.74 97.2% 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 Sat Oct 8 2011 at 14:21:06 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3028 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.767652 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): -35.03700 14.15100 ymin,ymax (A): -15.46600 35.64400 zmin,zma (A): -45.32500 12.55800 x,y,z range (A): 49.18800 51.11000 57.88300 scale (grids/A): 2.767652 object centre (A): -10.44300 10.08900 -16.38350 number of atom coordinates read : 3028 total number of charged atoms : 2881 net assigned charge : 7.1674585E-06 assigned positive charge : 453.4966 centred at (gu) : 82.06726 85.70296 76.60899 assigned negative charge : -453.4973 centred at (gu) : 81.84396 85.55034 77.03307 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 190954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24106 grid for indexing accessible points = 1.400000 m= 95766 mr = 143556 m= 31461 mr = 79167 m= 6453 mr = 25037 m= 659 mr = 4600 m= 19 mr = 383 m= 0 mr = 6 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 72563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 23047 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) : 1.845101 object centre at (A) : -10.44300 10.08900 -16.38350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7140551 -0.2770363 midg,1,midg; midg,igrid,midg 9.4919853E-02 7.6972052E-02 1,midg,midg; igrid,midg,midg -7.2149053E-02 1.7965795E-02 gauss-seidel spectral radius is 0.9992467 estimated iterations to convergence 288 setup time was (sec) 1.900000 now iterating at: 14:21:08 rms-change max change #iterations 10.36843 341.7177 at 10iterations 6.028543 124.2079 at 20iterations 3.486689 62.97518 at 30iterations 2.009743 41.67711 at 40iterations 1.152256 23.77570 at 50iterations 0.6616573 13.31818 at 60iterations 0.3799610 6.654123 at 70iterations 0.2181174 3.856590 at 80iterations 0.1248816 2.381777 at 90iterations 7.1667939E-02 1.179087 at 100iterations 4.1003086E-02 0.7297421 at 110iterations 2.3516113E-02 0.3933945 at 120iterations 1.3464161E-02 0.2371140 at 130iterations 7.6985168E-03 0.1309166 at 140iterations 4.4204690E-03 8.3580017E-02 at 150iterations 2.5364738E-03 4.3383598E-02 at 160iterations 1.4553439E-03 2.7091265E-02 at 170iterations 8.3710504E-04 1.5697479E-02 at 180iterations finished qdiffx linear iterations at : 14:21:22 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 8.3710504E-04 1.5697479E-02 energy calculations done at 15.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.13000 DelPhi exited at 14:21:23 16.127u 0.314s 0:16.73 98.2% 0+0k 0+0io 0pf+0w