Sat Oct 8 18:41:19 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 18:41:19 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! 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: ZN5 501 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6322482 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): -31.89000 17.56900 ymin,ymax (A): -23.79700 22.34400 zmin,zma (A): -11.97500 44.33200 x,y,z range (A): 49.45900 46.14100 56.30700 scale (grids/A): 0.6322482 object centre (A): -7.160501 -0.7264996 16.17850 number of atom coordinates read : 2601 total number of charged atoms : 2482 net assigned charge : 4.500006 assigned positive charge : 395.8250 centred at (gu) : 88.47356 89.47327 89.89706 assigned negative charge : -391.3255 centred at (gu) : 88.37588 89.50980 89.78197 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6886 nv = 96 ne = 84 npr = 53648 no. pairs analyzed = 53648 no. exposed pairs = 2999 no. arc points = 21537 no. surface atoms = 1017 nbur = 1584 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3913 m= 0 mr = 54 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.3500000 number of dielectric boundary points 3270 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2101 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7970029E-09 1.5786780E-08 midg,1,midg; midg,igrid,midg 9.8803641E-09 1.7262655E-09 1,midg,midg; igrid,midg,midg -5.7187868E-09 1.0477184E-08 gauss-seidel spectral radius is 0.9870383 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 18:41:20 rms-change max change #iterations 0.1406402 23.25958 at 10iterations 1.3469615E-02 2.017553 at 20iterations 1.3056860E-03 0.1713293 at 30iterations 1.2403932E-04 2.7137756E-02 at 40iterations 1.2133149E-05 1.7013550E-03 at 50iterations finished qdiffx linear iterations at : 18:41:23 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 1.2133149E-05 1.7013550E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 18:41:24 3.672u 0.210s 0:04.23 91.7% 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 18:41:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! 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: ZN5 501 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: 1.896745 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): -31.89000 17.56900 ymin,ymax (A): -23.79700 22.34400 zmin,zma (A): -11.97500 44.33200 x,y,z range (A): 49.45900 46.14100 56.30700 scale (grids/A): 1.896745 object centre (A): -7.160501 -0.7264996 16.17850 number of atom coordinates read : 2601 total number of charged atoms : 2482 net assigned charge : 4.500006 assigned positive charge : 395.8250 centred at (gu) : 85.42039 88.41934 89.69081 assigned negative charge : -391.3255 centred at (gu) : 85.12747 88.52893 89.34558 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21537 grid for indexing accessible points = 1.400000 m= 27150 mr = 52456 m= 4003 mr = 20496 m= 239 mr = 2500 m= 2 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5399 time to turn everything in is 0.5500000 number of dielectric boundary points 30436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19556 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) : 0.6322482 object centre at (A) : -7.160501 -0.7264996 16.17850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2303099E-02 3.4663476E-02 midg,1,midg; midg,igrid,midg 1.3581848E-02 2.0086425E-03 1,midg,midg; igrid,midg,midg -1.5037626E-03 3.9580423E-02 gauss-seidel spectral radius is 0.9986200 estimated iterations to convergence 213 setup time was (sec) 0.8700000 now iterating at: 18:41:25 rms-change max change #iterations 4.227043 170.9937 at 10iterations 1.968054 72.63955 at 20iterations 0.9180346 34.76929 at 30iterations 0.4267803 13.13225 at 40iterations 0.2003290 7.277218 at 50iterations 9.3298957E-02 3.034325 at 60iterations 4.3507811E-02 1.356354 at 70iterations 2.0345312E-02 0.6504573 at 80iterations 9.4493115E-03 0.3221273 at 90iterations 4.4212053E-03 0.1392078 at 100iterations 2.0661734E-03 6.1872482E-02 at 110iterations 9.6346810E-04 2.9331446E-02 at 120iterations finished qdiffx linear iterations at : 18:41:32 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 9.6346810E-04 2.9331446E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 18:41:33 8.301u 0.270s 0:08.83 97.0% 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 18:41:33 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! 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: ZN5 501 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.845117 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): -31.89000 17.56900 ymin,ymax (A): -23.79700 22.34400 zmin,zma (A): -11.97500 44.33200 x,y,z range (A): 49.45900 46.14100 56.30700 scale (grids/A): 2.845117 object centre (A): -7.160501 -0.7264996 16.17850 number of atom coordinates read : 2601 total number of charged atoms : 2482 net assigned charge : 4.500006 assigned positive charge : 395.8250 centred at (gu) : 83.13055 87.62898 89.53606 assigned negative charge : -391.3255 centred at (gu) : 82.69115 87.79341 89.01829 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 172352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21537 grid for indexing accessible points = 1.400000 m= 88780 mr = 126746 m= 31246 mr = 73692 m= 7084 mr = 25407 m= 1003 mr = 5377 m= 65 mr = 736 m= 0 mr = 28 time to grow re-entrant surface = 0.7699999 no. cavity mid-points inaccessible to solvent = 17986 time to turn everything in is 1.330000 number of dielectric boundary points 68544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 19854 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) : 1.896745 object centre at (A) : -7.160501 -0.7264996 16.17850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1523858 0.3951352 midg,1,midg; midg,igrid,midg 0.1676410 -1.8017860E-03 1,midg,midg; igrid,midg,midg 2.2418074E-02 0.4798107 gauss-seidel spectral radius is 0.9992490 estimated iterations to convergence 288 setup time was (sec) 1.670000 now iterating at: 18:41:34 rms-change max change #iterations 9.863694 376.0491 at 10iterations 5.704736 137.1389 at 20iterations 3.266143 93.29184 at 30iterations 1.876900 37.30032 at 40iterations 1.075469 20.30512 at 50iterations 0.6169569 13.46071 at 60iterations 0.3529208 6.599201 at 70iterations 0.2020014 3.796740 at 80iterations 0.1156273 2.479080 at 90iterations 6.6164248E-02 1.347725 at 100iterations 3.7889726E-02 0.6919823 at 110iterations 2.1671202E-02 0.4331474 at 120iterations 1.2410828E-02 0.2200546 at 130iterations 7.0789331E-03 0.1299362 at 140iterations 4.0586852E-03 7.1821690E-02 at 150iterations 2.3172202E-03 4.3327332E-02 at 160iterations 1.3241824E-03 2.5655746E-02 at 170iterations 7.5648929E-04 1.3488770E-02 at 180iterations finished qdiffx linear iterations at : 18:41:46 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 7.5648929E-04 1.3488770E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 18:41:47 13.510u 0.270s 0:14.06 98.0% 0+0k 0+0io 0pf+0w