Sat Oct 15 12:53:43 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 15 2011 at 12:53:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 0.5935312 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): -49.87800 10.10200 ymin,ymax (A): -25.10700 26.70700 zmin,zma (A): -29.68100 26.46300 x,y,z range (A): 59.98000 51.81400 56.14400 scale (grids/A): 0.5935312 object centre (A): -19.88800 0.8000002 -1.609000 number of atom coordinates read : 2869 total number of charged atoms : 2799 net assigned charge : 4.500016 assigned positive charge : 429.6180 centred at (gu) : 89.75761 90.62988 91.62220 assigned negative charge : -425.1198 centred at (gu) : 89.76748 90.55766 91.54340 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7093 nv = 96 ne = 84 npr = 54190 no. pairs analyzed = 54190 no. exposed pairs = 4058 no. arc points = 28963 no. surface atoms = 1345 nbur = 1524 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 386 mr = 3539 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3407708E-10 5.8673675E-09 midg,1,midg; midg,igrid,midg -7.5033962E-10 4.4161470E-09 1,midg,midg; igrid,midg,midg 1.9121558E-09 1.1088874E-09 gauss-seidel spectral radius is 0.9853527 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 12:53:49 rms-change max change #iterations 0.1063067 20.52534 at 10iterations 9.0848776E-03 1.366776 at 20iterations 9.5203996E-04 0.1306458 at 30iterations 1.7596064E-04 2.7558804E-02 at 40iterations 4.5506164E-05 7.4374676E-03 at 50iterations finished qdiffx linear iterations at : 12:53:57 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 4.5506164E-05 7.4374676E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 12:53:59 3.143u 0.158s 0:13.40 24.5% 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 15 2011 at 12:54:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 1.780594 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): -49.87800 10.10200 ymin,ymax (A): -25.10700 26.70700 zmin,zma (A): -29.68100 26.46300 x,y,z range (A): 59.98000 51.81400 56.14400 scale (grids/A): 1.780594 object centre (A): -19.88800 0.8000002 -1.609000 number of atom coordinates read : 2869 total number of charged atoms : 2799 net assigned charge : 4.500016 assigned positive charge : 429.6180 centred at (gu) : 89.27192 91.88864 94.86569 assigned negative charge : -425.1198 centred at (gu) : 89.30255 91.67262 94.63009 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 76895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28963 grid for indexing accessible points = 1.400000 m= 27065 mr = 50859 m= 4105 mr = 18677 m= 205 mr = 2312 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 36375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21856 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) : 0.5935312 object centre at (A) : -19.88800 0.8000002 -1.609000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1873697E-03 1.5059841E-02 midg,1,midg; midg,igrid,midg 1.1805296E-02 3.1274579E-02 1,midg,midg; igrid,midg,midg 1.5361160E-02 -1.9767938E-02 gauss-seidel spectral radius is 0.9985003 estimated iterations to convergence 205 setup time was (sec) 0.8200000 now iterating at: 12:54:07 rms-change max change #iterations 3.895943 171.5910 at 10iterations 1.755379 63.49882 at 20iterations 0.7909560 27.22819 at 30iterations 0.3556417 12.49152 at 40iterations 0.1606956 5.210796 at 50iterations 7.2486296E-02 2.406767 at 60iterations 3.2612190E-02 1.114532 at 70iterations 1.4772099E-02 0.4985504 at 80iterations 6.7191073E-03 0.2253170 at 90iterations 3.0350131E-03 0.1032448 at 100iterations 1.3859329E-03 4.5910358E-02 at 110iterations 6.3969445E-04 2.0643234E-02 at 120iterations finished qdiffx linear iterations at : 12:54:26 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 6.3969445E-04 2.0643234E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 12:54:28 7.245u 0.238s 0:26.48 28.2% 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 15 2011 at 12:54:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 2.670890 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): -49.87800 10.10200 ymin,ymax (A): -25.10700 26.70700 zmin,zma (A): -29.68100 26.46300 x,y,z range (A): 59.98000 51.81400 56.14400 scale (grids/A): 2.670890 object centre (A): -19.88800 0.8000002 -1.609000 number of atom coordinates read : 2869 total number of charged atoms : 2799 net assigned charge : 4.500016 assigned positive charge : 429.6180 centred at (gu) : 88.90769 92.83295 97.29827 assigned negative charge : -425.1198 centred at (gu) : 88.95385 92.50885 96.94518 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 178038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28963 grid for indexing accessible points = 1.400000 m= 87105 mr = 124619 m= 31071 mr = 68268 m= 7211 mr = 23876 m= 881 mr = 4915 m= 47 mr = 515 m= 0 mr = 4 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 82156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 22385 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) : 1.780594 object centre at (A) : -19.88800 0.8000002 -1.609000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7109596E-02 0.1700406 midg,1,midg; midg,igrid,midg 0.2174848 0.4215568 1,midg,midg; igrid,midg,midg 0.2601593 -0.3170962 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 1.730000 now iterating at: 12:54:33 rms-change max change #iterations 9.751636 339.1237 at 10iterations 5.789279 138.8733 at 20iterations 3.385826 95.79510 at 30iterations 1.975454 42.30824 at 40iterations 1.143824 23.24950 at 50iterations 0.6617713 13.07497 at 60iterations 0.3810810 8.573566 at 70iterations 0.2191033 4.208572 at 80iterations 0.1261278 2.543346 at 90iterations 7.2165079E-02 1.440334 at 100iterations 4.1410699E-02 0.8285699 at 110iterations 2.3712892E-02 0.4430542 at 120iterations 1.3592389E-02 0.2646065 at 130iterations 7.7664293E-03 0.1505852 at 140iterations 4.4564153E-03 7.8857422E-02 at 150iterations 2.5486730E-03 4.9522400E-02 at 160iterations 1.4563672E-03 2.6877403E-02 at 170iterations 8.3739561E-04 1.6584396E-02 at 180iterations finished qdiffx linear iterations at : 12:55:01 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 8.3739561E-04 1.6584396E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 12:55:03 13.429u 0.227s 0:33.18 41.1% 0+0k 0+0io 0pf+0w