Mon Oct 10 14:01:41 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+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 Mon Oct 10 2011 at 14:01:41 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 = 2116 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: 0.6342533 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): 69.57500 125.7040 ymin,ymax (A): -8.046000 37.55700 zmin,zma (A): 3.446000 52.13800 x,y,z range (A): 56.12900 45.60300 48.69200 scale (grids/A): 0.6342533 object centre (A): 97.63950 14.75550 27.79200 number of atom coordinates read : 2116 total number of charged atoms : 2048 net assigned charge : -0.4999697 assigned positive charge : 315.2826 centred at (gu) : 90.37810 88.99148 88.99674 assigned negative charge : -315.7834 centred at (gu) : 90.42167 89.06673 89.09782 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5808 nv = 96 ne = 84 npr = 41260 no. pairs analyzed = 41260 no. exposed pairs = 2998 no. arc points = 20547 no. surface atoms = 1002 nbur = 1114 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 2927 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1600000 number of dielectric boundary points 3175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1989 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1679588E-09 -7.2519253E-09 midg,1,midg; midg,igrid,midg 6.6168386E-09 -5.5352150E-09 1,midg,midg; igrid,midg,midg 2.5328994E-09 -4.6677173E-09 gauss-seidel spectral radius is 0.9870893 estimated iterations to convergence 72 setup time was (sec) 0.3600000 now iterating at: 14:01:41 rms-change max change #iterations 0.1244689 20.45222 at 10iterations 1.1981784E-02 1.905621 at 20iterations 1.1527728E-03 0.2083807 at 30iterations 1.1157722E-04 1.8753052E-02 at 40iterations 1.0993424E-05 1.6632080E-03 at 50iterations finished qdiffx linear iterations at : 14:01:44 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.0993424E-05 1.6632080E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:01:45 3.362u 0.172s 0:04.30 82.0% 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 Mon Oct 10 2011 at 14:01:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 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: 1.902760 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): 69.57500 125.7040 ymin,ymax (A): -8.046000 37.55700 zmin,zma (A): 3.446000 52.13800 x,y,z range (A): 56.12900 45.60300 48.69200 scale (grids/A): 1.902760 object centre (A): 97.63950 14.75550 27.79200 number of atom coordinates read : 2116 total number of charged atoms : 2048 net assigned charge : -0.4999697 assigned positive charge : 315.2826 centred at (gu) : 91.13406 86.97414 86.98993 assigned negative charge : -315.7834 centred at (gu) : 91.26536 87.20026 87.29359 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20547 grid for indexing accessible points = 1.400000 m= 22376 mr = 40776 m= 3980 mr = 15882 m= 291 mr = 2544 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 297 time to turn everything in is 0.3300000 number of dielectric boundary points 29310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 16134 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) : 0.6342533 object centre at (A) : 97.63950 14.75550 27.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1368524E-02 7.9682451E-03 midg,1,midg; midg,igrid,midg 7.8780130E-03 -6.5765320E-03 1,midg,midg; igrid,midg,midg -3.5372950E-02 -1.4607323E-02 gauss-seidel spectral radius is 0.9985937 estimated iterations to convergence 211 setup time was (sec) 0.5400000 now iterating at: 14:01:46 rms-change max change #iterations 3.770563 162.9815 at 10iterations 1.739456 61.25330 at 20iterations 0.8077466 30.37461 at 30iterations 0.3731208 12.92584 at 40iterations 0.1727748 6.167175 at 50iterations 8.0104724E-02 2.628479 at 60iterations 3.7033211E-02 1.244387 at 70iterations 1.7179118E-02 0.5983295 at 80iterations 7.9588871E-03 0.2726674 at 90iterations 3.6874565E-03 0.1209888 at 100iterations 1.7080571E-03 6.2560081E-02 at 110iterations 7.9376891E-04 2.6041031E-02 at 120iterations finished qdiffx linear iterations at : 14:01:53 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 7.9376891E-04 2.6041031E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 14:01:54 7.790u 0.200s 0:08.80 90.7% 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 Mon Oct 10 2011 at 14:01:54 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 = 2116 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: 2.854140 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): 69.57500 125.7040 ymin,ymax (A): -8.046000 37.55700 zmin,zma (A): 3.446000 52.13800 x,y,z range (A): 56.12900 45.60300 48.69200 scale (grids/A): 2.854140 object centre (A): 97.63950 14.75550 27.79200 number of atom coordinates read : 2116 total number of charged atoms : 2048 net assigned charge : -0.4999697 assigned positive charge : 315.2826 centred at (gu) : 91.70106 85.46108 85.48491 assigned negative charge : -315.7834 centred at (gu) : 91.89809 85.80038 85.94051 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 143223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20547 grid for indexing accessible points = 1.400000 m= 70226 mr = 99361 m= 27254 mr = 55709 m= 7291 mr = 21559 m= 1243 mr = 5591 m= 89 mr = 908 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1039 time to turn everything in is 0.8300000 number of dielectric boundary points 66149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 16384 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) : 1.902760 object centre at (A) : 97.63950 14.75550 27.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3187630 0.1166264 midg,1,midg; midg,igrid,midg 0.1117297 -4.5586605E-02 1,midg,midg; igrid,midg,midg -0.7241998 -0.1970215 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.060000 now iterating at: 14:01:55 rms-change max change #iterations 8.944421 395.9069 at 10iterations 5.208240 126.4717 at 20iterations 3.009599 65.82619 at 30iterations 1.734986 36.90122 at 40iterations 0.9997085 20.46524 at 50iterations 0.5751002 12.41365 at 60iterations 0.3302956 6.538771 at 70iterations 0.1893486 4.035425 at 80iterations 0.1084654 2.312573 at 90iterations 6.2111415E-02 1.264755 at 100iterations 3.5614349E-02 0.7054195 at 110iterations 2.0339467E-02 0.4646959 at 120iterations 1.1660899E-02 0.2362051 at 130iterations 6.6609373E-03 0.1340351 at 140iterations 3.8095966E-03 7.0617676E-02 at 150iterations 2.1824411E-03 4.6725273E-02 at 160iterations 1.2453261E-03 2.4185181E-02 at 170iterations 7.1302336E-04 1.4606476E-02 at 180iterations finished qdiffx linear iterations at : 14:02:06 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 7.1302336E-04 1.4606476E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 14:02:07 12.331u 0.196s 0:13.46 93.0% 0+0k 0+0io 0pf+0w