Mon Oct 10 11:10:05 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 Mon Oct 10 2011 at 11:10:05 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2119 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7464877 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): -20.95200 24.22300 ymin,ymax (A): -8.012000 36.30200 zmin,zma (A): -3.471000 44.21900 x,y,z range (A): 45.17500 44.31400 47.69000 scale (grids/A): 0.7464877 object centre (A): 1.635500 14.14500 20.37400 number of atom coordinates read : 2119 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 89.00214 90.44917 90.18883 assigned negative charge : -324.1720 centred at (gu) : 89.02602 90.53598 90.38215 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8131 nv = 96 ne = 84 npr = 43893 no. pairs analyzed = 43893 no. exposed pairs = 2677 no. arc points = 19128 no. surface atoms = 904 nbur = 1215 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 557 mr = 4510 m= 2 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2700000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2810026E-08 -3.6963073E-07 midg,1,midg; midg,igrid,midg -2.3650840E-08 -2.4834657E-07 1,midg,midg; igrid,midg,midg -1.1691307E-07 -1.2876905E-07 gauss-seidel spectral radius is 0.9906487 estimated iterations to convergence 84 setup time was (sec) 0.5800000 now iterating at: 11:10:06 rms-change max change #iterations 0.2583258 41.22851 at 10iterations 3.5145573E-02 4.547141 at 20iterations 4.8017874E-03 0.6895061 at 30iterations 6.4729457E-04 8.4901810E-02 at 40iterations 9.0652822E-05 1.1468410E-02 at 50iterations finished qdiffx linear iterations at : 11:10:10 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 9.0652822E-05 1.1468410E-02 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 11:10:10 4.849u 0.377s 0:05.50 94.7% 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 11:10:10 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2119 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.239463 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): -20.95200 24.22300 ymin,ymax (A): -8.012000 36.30200 zmin,zma (A): -3.471000 44.21900 x,y,z range (A): 45.17500 44.31400 47.69000 scale (grids/A): 2.239463 object centre (A): 1.635500 14.14500 20.37400 number of atom coordinates read : 2119 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 87.00646 91.34756 90.56610 assigned negative charge : -324.1720 centred at (gu) : 87.07805 91.60796 91.14635 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19128 grid for indexing accessible points = 1.400000 m= 34291 mr = 58985 m= 7422 mr = 26130 m= 852 mr = 5222 m= 26 mr = 485 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.7200000 number of dielectric boundary points 37227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15766 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) : 0.7464877 object centre at (A) : 1.635500 14.14500 20.37400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1140634E-03 -0.1441676 midg,1,midg; midg,igrid,midg -2.7084960E-02 -3.7704993E-02 1,midg,midg; igrid,midg,midg 2.1129032E-03 -9.7464575E-03 gauss-seidel spectral radius is 0.9989423 estimated iterations to convergence 243 setup time was (sec) 1.070000 now iterating at: 11:10:12 rms-change max change #iterations 5.236631 204.7413 at 10iterations 2.671728 91.74434 at 20iterations 1.368480 37.64462 at 30iterations 0.7008224 19.41090 at 40iterations 0.3584735 9.612559 at 50iterations 0.1846590 5.540409 at 60iterations 9.4193064E-02 2.626561 at 70iterations 4.8266675E-02 1.312725 at 80iterations 2.4752002E-02 0.6724091 at 90iterations 1.2676764E-02 0.3712306 at 100iterations 6.4934739E-03 0.1685772 at 110iterations 3.3193075E-03 0.1129620 at 120iterations finished qdiffx linear iterations at : 11:10:22 total time elapsed so far: 11.61000 # loops : 120 mean,max change (kT/e) : 3.3193075E-03 0.1129620 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 11:10:23 11.784u 0.438s 0:12.59 96.9% 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 11:10:23 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2119 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.359195 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): -20.95200 24.22300 ymin,ymax (A): -8.012000 36.30200 zmin,zma (A): -3.471000 44.21900 x,y,z range (A): 45.17500 44.31400 47.69000 scale (grids/A): 3.359195 object centre (A): 1.635500 14.14500 20.37400 number of atom coordinates read : 2119 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 85.50994 92.02130 90.84932 assigned negative charge : -324.1720 centred at (gu) : 85.61724 92.41195 91.71951 start vw surface at 0.1000000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 196835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19128 grid for indexing accessible points = 1.400000 m= 105451 mr = 142328 m= 45067 mr = 87497 m= 14277 mr = 37298 m= 3404 mr = 11431 m= 498 mr = 2684 m= 22 mr = 338 m= 0 mr = 14 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 2.230000 number of dielectric boundary points 83964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 15824 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) : 2.239463 object centre at (A) : 1.635500 14.14500 20.37400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2256146E-02 -1.295471 midg,1,midg; midg,igrid,midg -0.2487778 -0.1675374 1,midg,midg; igrid,midg,midg 8.8611625E-02 -0.1454995 gauss-seidel spectral radius is 0.9993241 estimated iterations to convergence 303 setup time was (sec) 2.580000 now iterating at: 11:10:26 rms-change max change #iterations 11.14562 275.9225 at 10iterations 6.585297 130.6587 at 20iterations 3.894725 65.72946 at 30iterations 2.293373 36.99659 at 40iterations 1.355852 24.38166 at 50iterations 0.7987422 14.21547 at 60iterations 0.4704408 7.120909 at 70iterations 0.2770263 4.689625 at 80iterations 0.1634513 2.783651 at 90iterations 9.6241169E-02 1.498581 at 100iterations 5.6661852E-02 0.8252854 at 110iterations 3.3276513E-02 0.4992994 at 120iterations 1.9560425E-02 0.3045883 at 130iterations 1.1530778E-02 0.1901596 at 140iterations 6.7935553E-03 0.1188288 at 150iterations 3.9973175E-03 6.0310364E-02 at 160iterations 2.3529150E-03 3.6157131E-02 at 170iterations 1.3834074E-03 2.0567894E-02 at 180iterations finished qdiffx linear iterations at : 11:10:44 total time elapsed so far: 20.78000 # loops : 180 mean,max change (kT/e) : 1.3834074E-03 2.0567894E-02 energy calculations done at 20.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.94000 DelPhi exited at 11:10:45 20.942u 0.480s 0:21.73 98.5% 0+0k 0+0io 0pf+0w