Tue Oct 11 06:00:35 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 06:00:35 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7070366 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): 25.61100 72.09400 ymin,ymax (A): -18.74000 31.61100 zmin,zma (A): 3.862000 46.30500 x,y,z range (A): 46.48300 50.35100 42.44300 scale (grids/A): 0.7070366 object centre (A): 48.85250 6.435500 25.08350 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 89.20901 90.17720 90.35934 assigned negative charge : -319.4310 centred at (gu) : 89.34135 90.11375 90.44391 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7216 nv = 96 ne = 84 npr = 42335 no. pairs analyzed = 42335 no. exposed pairs = 2581 no. arc points = 17426 no. surface atoms = 888 nbur = 1430 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4194 m= 3 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1599 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5209173E-08 6.7231780E-09 midg,1,midg; midg,igrid,midg 1.6728796E-08 8.3694708E-08 1,midg,midg; igrid,midg,midg 1.3398137E-07 -1.4989329E-08 gauss-seidel spectral radius is 0.9895756 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:00:36 rms-change max change #iterations 0.2046327 29.54874 at 10iterations 2.5742866E-02 3.152534 at 20iterations 3.6105022E-03 0.4544182 at 30iterations 6.7753560E-04 7.9284668E-02 at 40iterations 1.8890551E-04 2.0713806E-02 at 50iterations finished qdiffx linear iterations at : 06:00:38 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.8890551E-04 2.0713806E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:00:39 3.310u 0.162s 0:04.00 86.7% 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 Tue Oct 11 2011 at 06:00:39 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.121110 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): 25.61100 72.09400 ymin,ymax (A): -18.74000 31.61100 zmin,zma (A): 3.862000 46.30500 x,y,z range (A): 46.48300 50.35100 42.44300 scale (grids/A): 2.121110 object centre (A): 48.85250 6.435500 25.08350 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 87.62721 90.53152 91.07803 assigned negative charge : -319.4310 centred at (gu) : 88.02410 90.34119 91.33171 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76469 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17426 grid for indexing accessible points = 1.400000 m= 31442 mr = 54672 m= 6055 mr = 24094 m= 568 mr = 3984 m= 18 mr = 279 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15782 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) : 0.7070366 object centre at (A) : 48.85250 6.435500 25.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0089891E-02 2.5415177E-02 midg,1,midg; midg,igrid,midg 3.8921885E-02 2.7067671E-02 1,midg,midg; igrid,midg,midg 4.3922450E-02 -4.8865113E-02 gauss-seidel spectral radius is 0.9988338 estimated iterations to convergence 232 setup time was (sec) 0.6100000 now iterating at: 06:00:40 rms-change max change #iterations 4.657429 170.1564 at 10iterations 2.302999 82.53479 at 20iterations 1.145144 37.55798 at 30iterations 0.5689978 16.45462 at 40iterations 0.2827594 9.218518 at 50iterations 0.1408610 4.483518 at 60iterations 7.0052765E-02 1.962709 at 70iterations 3.4914251E-02 0.9932690 at 80iterations 1.7514803E-02 0.5478001 at 90iterations 8.8318260E-03 0.2688370 at 100iterations 4.4849413E-03 0.1253929 at 110iterations 2.3406267E-03 8.0490112E-02 at 120iterations finished qdiffx linear iterations at : 06:00:47 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.3406267E-03 8.0490112E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 06:00:47 7.721u 0.174s 0:08.23 95.8% 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 06:00:48 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.181665 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): 25.61100 72.09400 ymin,ymax (A): -18.74000 31.61100 zmin,zma (A): 3.862000 46.30500 x,y,z range (A): 46.48300 50.35100 42.44300 scale (grids/A): 3.181665 object centre (A): 48.85250 6.435500 25.08350 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 86.44079 90.79733 91.61703 assigned negative charge : -319.4310 centred at (gu) : 87.03625 90.51185 91.99745 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 176515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17426 grid for indexing accessible points = 1.400000 m= 97691 mr = 131810 m= 39924 mr = 81709 m= 11364 mr = 32977 m= 2251 mr = 8792 m= 279 mr = 1600 m= 15 mr = 170 m= 0 mr = 5 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15904 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) : 2.121110 object centre at (A) : 48.85250 6.435500 25.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1177911 0.2164641 midg,1,midg; midg,igrid,midg 0.2749212 0.1085894 1,midg,midg; igrid,midg,midg 0.4429533 -0.6064571 gauss-seidel spectral radius is 0.9992986 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 06:00:50 rms-change max change #iterations 10.40436 374.6088 at 10iterations 6.173309 152.3471 at 20iterations 3.660750 73.52856 at 30iterations 2.163846 42.80923 at 40iterations 1.274773 25.05438 at 50iterations 0.7519116 14.36990 at 60iterations 0.4418436 8.206825 at 70iterations 0.2596202 4.572052 at 80iterations 0.1526752 2.550323 at 90iterations 8.9611307E-02 1.721292 at 100iterations 5.2840162E-02 0.9382381 at 110iterations 3.1298511E-02 0.5193024 at 120iterations 1.8699624E-02 0.3498154 at 130iterations 1.1400631E-02 0.2445755 at 140iterations 7.1500815E-03 0.1434059 at 150iterations 4.6680518E-03 8.9221954E-02 at 160iterations 3.2304937E-03 6.7695618E-02 at 170iterations 2.3646448E-03 4.6691895E-02 at 180iterations finished qdiffx linear iterations at : 06:01:01 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 2.3646448E-03 4.6691895E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 06:01:01 12.730u 0.198s 0:13.47 95.9% 0+0k 0+0io 0pf+0w