Tue Oct 11 06:39:41 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 06:39:42 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6853271 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): -20.64300 24.53600 ymin,ymax (A): -27.68200 12.14100 zmin,zma (A): -15.73200 36.21400 x,y,z range (A): 45.17900 39.82300 51.94600 scale (grids/A): 0.6853271 object centre (A): 1.946501 -7.770500 10.24100 number of atom coordinates read : 2053 total number of charged atoms : 1932 net assigned charge : 5.931010 assigned positive charge : 312.7770 centred at (gu) : 90.02592 90.68977 90.06818 assigned negative charge : -306.8462 centred at (gu) : 89.88263 90.66663 90.01884 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6502 nv = 96 ne = 84 npr = 41170 no. pairs analyzed = 41170 no. exposed pairs = 2458 no. arc points = 16975 no. surface atoms = 835 nbur = 1218 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3698 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1689 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7508 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4471206E-08 4.4084921E-08 midg,1,midg; midg,igrid,midg 1.9630466E-08 4.1108109E-08 1,midg,midg; igrid,midg,midg -1.3280902E-08 7.0786754E-08 gauss-seidel spectral radius is 0.9889056 estimated iterations to convergence 77 setup time was (sec) 0.5000000 now iterating at: 06:39:42 rms-change max change #iterations 0.1763770 26.06644 at 10iterations 2.0382177E-02 2.813713 at 20iterations 2.5385052E-03 0.3581266 at 30iterations 3.6560942E-04 5.3604126E-02 at 40iterations 7.4790711E-05 9.6435547E-03 at 50iterations finished qdiffx linear iterations at : 06:39:45 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 7.4790711E-05 9.6435547E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 06:39:45 3.095u 0.149s 0:03.54 91.2% 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 Tue Oct 11 2011 at 06:39:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.055981 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): -20.64300 24.53600 ymin,ymax (A): -27.68200 12.14100 zmin,zma (A): -15.73200 36.21400 x,y,z range (A): 45.17900 39.82300 51.94600 scale (grids/A): 2.055981 object centre (A): 1.946501 -7.770500 10.24100 number of atom coordinates read : 2053 total number of charged atoms : 1932 net assigned charge : 5.931010 assigned positive charge : 312.7770 centred at (gu) : 90.07777 92.06914 90.20453 assigned negative charge : -306.8462 centred at (gu) : 89.64803 91.99995 90.05667 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16975 grid for indexing accessible points = 1.400000 m= 26777 mr = 49114 m= 4771 mr = 20220 m= 386 mr = 3053 m= 2 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 28838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 15324 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) : 0.6853271 object centre at (A) : 1.946501 -7.770500 10.24100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6163087E-02 4.2183075E-02 midg,1,midg; midg,igrid,midg 5.2051609E-03 2.5911989E-02 1,midg,midg; igrid,midg,midg -1.9833627E-04 2.5396526E-02 gauss-seidel spectral radius is 0.9987612 estimated iterations to convergence 225 setup time was (sec) 0.7700000 now iterating at: 06:39:46 rms-change max change #iterations 4.334131 178.8478 at 10iterations 2.097089 86.70171 at 20iterations 1.019800 32.53544 at 30iterations 0.4984113 16.24920 at 40iterations 0.2417978 8.669281 at 50iterations 0.1173279 3.609790 at 60iterations 5.7204638E-02 1.887724 at 70iterations 2.7879953E-02 0.8973923 at 80iterations 1.3578195E-02 0.4120483 at 90iterations 6.6390601E-03 0.1964874 at 100iterations 3.2631771E-03 0.1022444 at 110iterations 1.6214326E-03 5.1494598E-02 at 120iterations finished qdiffx linear iterations at : 06:39:52 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 1.6214326E-03 5.1494598E-02 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 06:39:53 6.822u 0.143s 0:07.55 92.1% 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 06:39:53 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.083972 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): -20.64300 24.53600 ymin,ymax (A): -27.68200 12.14100 zmin,zma (A): -15.73200 36.21400 x,y,z range (A): 45.17900 39.82300 51.94600 scale (grids/A): 3.083972 object centre (A): 1.946501 -7.770500 10.24100 number of atom coordinates read : 2053 total number of charged atoms : 1932 net assigned charge : 5.931010 assigned positive charge : 312.7770 centred at (gu) : 90.11668 93.10365 90.30677 assigned negative charge : -306.8462 centred at (gu) : 89.47205 92.99987 90.08503 start vw surface at 0.1300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 160280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16975 grid for indexing accessible points = 1.400000 m= 84883 mr = 118562 m= 32988 mr = 70279 m= 8974 mr = 26960 m= 1548 mr = 6774 m= 161 mr = 1117 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 65049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 15456 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) : 2.055981 object centre at (A) : 1.946501 -7.770500 10.24100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8350518 0.3952527 midg,1,midg; midg,igrid,midg 3.6220003E-02 0.2080177 1,midg,midg; igrid,midg,midg 6.1179589E-02 0.2076043 gauss-seidel spectral radius is 0.9992756 estimated iterations to convergence 293 setup time was (sec) 1.810000 now iterating at: 06:39:55 rms-change max change #iterations 9.770469 326.5284 at 10iterations 5.713500 123.9314 at 20iterations 3.349113 63.50156 at 30iterations 1.951868 41.38404 at 40iterations 1.140972 21.38794 at 50iterations 0.6644183 13.41726 at 60iterations 0.3859010 7.639592 at 70iterations 0.2246700 4.033045 at 80iterations 0.1304589 2.454456 at 90iterations 7.5943723E-02 1.494617 at 100iterations 4.4250444E-02 0.7668152 at 110iterations 2.5891157E-02 0.4685345 at 120iterations 1.5172785E-02 0.2779694 at 130iterations 9.0018827E-03 0.1690578 at 140iterations 5.4452792E-03 0.1019449 at 150iterations 3.3900505E-03 6.4968109E-02 at 160iterations 2.1962447E-03 4.4227600E-02 at 170iterations 1.4992225E-03 2.8427124E-02 at 180iterations finished qdiffx linear iterations at : 06:40:05 total time elapsed so far: 11.69000 # loops : 180 mean,max change (kT/e) : 1.4992225E-03 2.8427124E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 06:40:05 11.865u 0.191s 0:12.47 96.6% 0+0k 0+0io 0pf+0w