Thu Jan 26 12:40:48 PST 2012 #!/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 Thu Jan 26 2012 at 12:40:48 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: LYS 236 has a net charge of 0.0200 !!! WARNING: GLN 239 has a net charge of 0.0170 !!! WARNING: GLN 244 has a net charge of 0.0170 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: 0.6292309 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): -11.25500 37.11200 ymin,ymax (A): -25.83300 24.24000 zmin,zma (A): -11.32300 45.25400 x,y,z range (A): 48.36700 50.07300 56.57700 scale (grids/A): 0.6292309 object centre (A): 12.92850 -0.7965002 16.96550 number of atom coordinates read : 2943 total number of charged atoms : 2802 net assigned charge : -2.945983 assigned positive charge : 449.0713 centred at (gu) : 89.66703 90.54160 91.64155 assigned negative charge : -452.0180 centred at (gu) : 89.50916 90.47806 91.68594 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7770 nv = 96 ne = 84 npr = 60341 no. pairs analyzed = 60341 no. exposed pairs = 3646 no. arc points = 24781 no. surface atoms = 1211 nbur = 1732 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 4398 m= 3 mr = 43 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 0.2700000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2514 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5975106E-10 -1.0721811E-08 midg,1,midg; midg,igrid,midg -8.3855802E-09 3.7862082E-09 1,midg,midg; igrid,midg,midg -2.0603416E-08 1.1681880E-08 gauss-seidel spectral radius is 0.9869426 estimated iterations to convergence 72 setup time was (sec) 0.4700000 now iterating at: 12:40:49 rms-change max change #iterations 0.1429622 22.56309 at 10iterations 1.3866589E-02 2.127317 at 20iterations 1.4041215E-03 0.1735954 at 30iterations 1.8617357E-04 2.5833130E-02 at 40iterations 4.4917382E-05 6.4911842E-03 at 50iterations finished qdiffx linear iterations at : 12:40:52 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 4.4917382E-05 6.4911842E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 12:40:52 3.558u 0.172s 0:04.16 89.4% 0+0k 0+45904io 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 Thu Jan 26 2012 at 12:40:52 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: LYS 236 has a net charge of 0.0200 !!! WARNING: GLN 239 has a net charge of 0.0170 !!! WARNING: GLN 244 has a net charge of 0.0170 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: 1.887693 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): -11.25500 37.11200 ymin,ymax (A): -25.83300 24.24000 zmin,zma (A): -11.32300 45.25400 x,y,z range (A): 48.36700 50.07300 56.57700 scale (grids/A): 1.887693 object centre (A): 12.92850 -0.7965002 16.96550 number of atom coordinates read : 2943 total number of charged atoms : 2802 net assigned charge : -2.945983 assigned positive charge : 449.0713 centred at (gu) : 89.00037 91.62418 94.92424 assigned negative charge : -452.0180 centred at (gu) : 88.52674 91.43359 95.05726 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24781 grid for indexing accessible points = 1.400000 m= 30163 mr = 59506 m= 4331 mr = 22239 m= 232 mr = 2569 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 462 time to turn everything in is 0.5100000 number of dielectric boundary points 34243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 21986 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) : 0.6292309 object centre at (A) : 12.92850 -0.7965002 16.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5885992E-03 -2.2557572E-02 midg,1,midg; midg,igrid,midg -1.6240820E-02 -5.9253071E-03 1,midg,midg; igrid,midg,midg -1.6924128E-02 2.8562902E-02 gauss-seidel spectral radius is 0.9986420 estimated iterations to convergence 215 setup time was (sec) 0.7200000 now iterating at: 12:40:53 rms-change max change #iterations 4.520953 175.5921 at 10iterations 2.123236 73.19537 at 20iterations 1.002337 31.55091 at 30iterations 0.4696611 15.62695 at 40iterations 0.2219439 6.788493 at 50iterations 0.1041120 3.172691 at 60iterations 4.9028594E-02 1.647354 at 70iterations 2.3029467E-02 0.6790171 at 80iterations 1.0856254E-02 0.3271856 at 90iterations 5.1179235E-03 0.1601629 at 100iterations 2.4277435E-03 6.8439484E-02 at 110iterations 1.1569136E-03 3.7353516E-02 at 120iterations finished qdiffx linear iterations at : 12:41:01 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 1.1569136E-03 3.7353516E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 12:41:01 8.099u 0.220s 0:08.67 95.8% 0+0k 0+45304io 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 Thu Jan 26 2012 at 12:41:01 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: LYS 236 has a net charge of 0.0200 !!! WARNING: GLN 239 has a net charge of 0.0170 !!! WARNING: GLN 244 has a net charge of 0.0170 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: 2.831539 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): -11.25500 37.11200 ymin,ymax (A): -25.83300 24.24000 zmin,zma (A): -11.32300 45.25400 x,y,z range (A): 48.36700 50.07300 56.57700 scale (grids/A): 2.831539 object centre (A): 12.92850 -0.7965002 16.96550 number of atom coordinates read : 2943 total number of charged atoms : 2802 net assigned charge : -2.945983 assigned positive charge : 449.0713 centred at (gu) : 88.50025 92.43607 97.38612 assigned negative charge : -452.0180 centred at (gu) : 87.79010 92.15035 97.58583 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 193985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24781 grid for indexing accessible points = 1.400000 m= 98895 mr = 143907 m= 34290 mr = 81257 m= 7645 mr = 27414 m= 975 mr = 5581 m= 53 mr = 624 m= 0 mr = 14 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1539 time to turn everything in is 1.360000 number of dielectric boundary points 77046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 22415 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) : 1.887693 object centre at (A) : 12.92850 -0.7965002 16.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1273781 1.9807303E-02 midg,1,midg; midg,igrid,midg -0.2126083 -5.9738252E-02 1,midg,midg; igrid,midg,midg -0.1093329 0.2508523 gauss-seidel spectral radius is 0.9992615 estimated iterations to convergence 290 setup time was (sec) 1.580000 now iterating at: 12:41:03 rms-change max change #iterations 10.64731 338.3769 at 10iterations 6.230930 137.5697 at 20iterations 3.635105 68.11778 at 30iterations 2.112237 44.45235 at 40iterations 1.222724 25.39387 at 50iterations 0.7088903 13.92042 at 60iterations 0.4105008 7.359592 at 70iterations 0.2367178 4.090412 at 80iterations 0.1366283 2.390623 at 90iterations 7.8853965E-02 1.382431 at 100iterations 4.5468386E-02 0.7640190 at 110iterations 2.6243361E-02 0.4811726 at 120iterations 1.5101386E-02 0.2520070 at 130iterations 8.7086605E-03 0.1524143 at 140iterations 5.0150319E-03 9.1499329E-02 at 150iterations 2.8963634E-03 5.4319382E-02 at 160iterations 1.6772633E-03 2.7854919E-02 at 170iterations 9.7263895E-04 1.7442703E-02 at 180iterations finished qdiffx linear iterations at : 12:41:15 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 9.7263895E-04 1.7442703E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 12:41:15 13.225u 0.224s 0:13.83 97.1% 0+0k 0+45296io 0pf+0w