Sat Oct 8 22:04:09 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 22:04:09 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2307 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6487826 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): -30.89900 23.97300 ymin,ymax (A): 28.18900 70.62000 zmin,zma (A): -13.43200 40.80000 x,y,z range (A): 54.87200 42.43100 54.23200 scale (grids/A): 0.6487826 object centre (A): -3.463000 49.40450 13.68400 number of atom coordinates read : 2307 total number of charged atoms : 2172 net assigned charge : 10.51402 assigned positive charge : 338.8985 centred at (gu) : 91.61564 91.31689 89.63789 assigned negative charge : -328.3851 centred at (gu) : 91.58743 91.18781 89.65314 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 45661 no. pairs analyzed = 45661 no. exposed pairs = 3102 no. arc points = 22122 no. surface atoms = 1040 nbur = 1267 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3503 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.1800000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2162 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2769925E-08 1.6119269E-08 midg,1,midg; midg,igrid,midg 2.4595956E-09 4.6306987E-08 1,midg,midg; igrid,midg,midg 1.1397759E-08 3.1803346E-08 gauss-seidel spectral radius is 0.9876738 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 22:04:09 rms-change max change #iterations 0.1420360 22.70710 at 10iterations 1.4479083E-02 1.987535 at 20iterations 1.5608238E-03 0.2329836 at 30iterations 1.9982159E-04 3.2936096E-02 at 40iterations 3.4836390E-05 6.7234039E-03 at 50iterations finished qdiffx linear iterations at : 22:04:12 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.4836390E-05 6.7234039E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 22:04:13 3.353u 0.190s 0:03.86 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 22:04:13 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2307 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.946348 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): -30.89900 23.97300 ymin,ymax (A): 28.18900 70.62000 zmin,zma (A): -13.43200 40.80000 x,y,z range (A): 54.87200 42.43100 54.23200 scale (grids/A): 1.946348 object centre (A): -3.463000 49.40450 13.68400 number of atom coordinates read : 2307 total number of charged atoms : 2172 net assigned charge : 10.51402 assigned positive charge : 338.8985 centred at (gu) : 94.84657 93.95029 88.91367 assigned negative charge : -328.3851 centred at (gu) : 94.76222 93.56367 88.95941 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 26393 mr = 47303 m= 4752 mr = 19226 m= 376 mr = 3058 m= 6 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1274 time to turn everything in is 0.3700000 number of dielectric boundary points 33141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17112 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) : 0.6487826 object centre at (A) : -3.463000 49.40450 13.68400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9339847E-02 4.9035493E-02 midg,1,midg; midg,igrid,midg -1.0644562E-02 3.1708155E-02 1,midg,midg; igrid,midg,midg 4.2531583E-02 3.2372244E-02 gauss-seidel spectral radius is 0.9986734 estimated iterations to convergence 218 setup time was (sec) 0.5700000 now iterating at: 22:04:14 rms-change max change #iterations 4.065273 216.5049 at 10iterations 1.920213 72.95591 at 20iterations 0.9040639 43.81920 at 30iterations 0.4259848 13.72216 at 40iterations 0.2010594 5.761494 at 50iterations 9.5711917E-02 3.063858 at 60iterations 4.5124765E-02 1.560286 at 70iterations 2.1370621E-02 0.7093163 at 80iterations 1.0132716E-02 0.3130856 at 90iterations 4.8256973E-03 0.1534481 at 100iterations 2.2930123E-03 7.8327179E-02 at 110iterations 1.0966874E-03 3.7529826E-02 at 120iterations finished qdiffx linear iterations at : 22:04:20 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.0966874E-03 3.7529826E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 22:04:21 7.688u 0.227s 0:08.31 95.0% 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 22:04:21 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2307 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.919522 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): -30.89900 23.97300 ymin,ymax (A): 28.18900 70.62000 zmin,zma (A): -13.43200 40.80000 x,y,z range (A): 54.87200 42.43100 54.23200 scale (grids/A): 2.919522 object centre (A): -3.463000 49.40450 13.68400 number of atom coordinates read : 2307 total number of charged atoms : 2172 net assigned charge : 10.51402 assigned positive charge : 338.8985 centred at (gu) : 97.26979 95.92523 88.37034 assigned negative charge : -328.3851 centred at (gu) : 97.14326 95.34551 88.43911 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 82805 mr = 115054 m= 32431 mr = 66726 m= 8729 mr = 26128 m= 1494 mr = 6637 m= 116 mr = 1047 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 0.9400000 number of dielectric boundary points 74774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 17376 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) : 1.946348 object centre at (A) : -3.463000 49.40450 13.68400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5552658 0.4736030 midg,1,midg; midg,igrid,midg -0.1166573 0.2917441 1,midg,midg; igrid,midg,midg 0.5687568 0.3812856 gauss-seidel spectral radius is 0.9992773 estimated iterations to convergence 294 setup time was (sec) 1.170000 now iterating at: 22:04:22 rms-change max change #iterations 9.762244 434.2820 at 10iterations 5.811334 141.1640 at 20iterations 3.434638 84.22318 at 30iterations 2.018174 45.55482 at 40iterations 1.180226 23.37667 at 50iterations 0.6904730 15.62536 at 60iterations 0.4031843 7.995024 at 70iterations 0.2343343 4.763142 at 80iterations 0.1363353 3.253212 at 90iterations 7.9124667E-02 1.627437 at 100iterations 4.5908239E-02 0.8149967 at 110iterations 2.6628289E-02 0.4871168 at 120iterations 1.5433045E-02 0.2849360 at 130iterations 8.9592393E-03 0.1597385 at 140iterations 5.1897811E-03 0.1017404 at 150iterations 3.0136777E-03 5.8581352E-02 at 160iterations 1.7492586E-03 3.4042358E-02 at 170iterations 1.0232715E-03 1.8756866E-02 at 180iterations finished qdiffx linear iterations at : 22:04:35 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 1.0232715E-03 1.8756866E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 22:04:35 12.499u 1.472s 0:14.23 98.1% 0+0k 0+0io 0pf+0w