Tue Oct 11 06:35:19 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 Tue Oct 11 2011 at 06:35:19 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 = 2077 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7107774 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): -20.83400 23.85900 ymin,ymax (A): -28.61700 10.96900 zmin,zma (A): -13.45800 36.62800 x,y,z range (A): 44.69300 39.58600 50.08600 scale (grids/A): 0.7107774 object centre (A): 1.512501 -8.824000 11.58500 number of atom coordinates read : 2077 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 90.50501 90.67088 89.23450 assigned negative charge : -308.6742 centred at (gu) : 90.36338 90.65332 89.15771 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7112 nv = 96 ne = 84 npr = 41840 no. pairs analyzed = 41840 no. exposed pairs = 2473 no. arc points = 16792 no. surface atoms = 847 nbur = 1230 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4163 m= 7 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1601 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0872797E-08 8.5809845E-08 midg,1,midg; midg,igrid,midg 4.4134421E-08 7.7688512E-08 1,midg,midg; igrid,midg,midg -1.4530552E-08 1.4638012E-07 gauss-seidel spectral radius is 0.9896798 estimated iterations to convergence 80 setup time was (sec) 0.3400000 now iterating at: 06:35:19 rms-change max change #iterations 0.2059805 31.35252 at 10iterations 2.5908235E-02 3.626140 at 20iterations 3.3475547E-03 0.3955307 at 30iterations 5.0433690E-04 6.8859100E-02 at 40iterations 1.0632974E-04 1.4266968E-02 at 50iterations finished qdiffx linear iterations at : 06:35:22 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.0632974E-04 1.4266968E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:35:23 3.304u 0.190s 0:04.52 77.2% 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 06:35:24 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 = 2077 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: 2.132332 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): -20.83400 23.85900 ymin,ymax (A): -28.61700 10.96900 zmin,zma (A): -13.45800 36.62800 x,y,z range (A): 44.69300 39.58600 50.08600 scale (grids/A): 2.132332 object centre (A): 1.512501 -8.824000 11.58500 number of atom coordinates read : 2077 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 91.51508 92.01260 87.70340 assigned negative charge : -308.6742 centred at (gu) : 91.09021 91.95990 87.47327 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16792 grid for indexing accessible points = 1.400000 m= 30294 mr = 54356 m= 5952 mr = 23079 m= 571 mr = 4013 m= 13 mr = 306 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 30821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15472 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) : 0.7107774 object centre at (A) : 1.512501 -8.824000 11.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5879407E-02 4.9204994E-02 midg,1,midg; midg,igrid,midg 5.4803230E-03 3.2244470E-02 1,midg,midg; igrid,midg,midg 1.5576554E-02 4.0426623E-02 gauss-seidel spectral radius is 0.9988386 estimated iterations to convergence 232 setup time was (sec) 0.6100000 now iterating at: 06:35:24 rms-change max change #iterations 4.587211 187.7663 at 10iterations 2.269738 75.69025 at 20iterations 1.136430 33.71964 at 30iterations 0.5631678 17.80433 at 40iterations 0.2809337 8.441078 at 50iterations 0.1401531 4.057419 at 60iterations 6.9510862E-02 2.044579 at 70iterations 3.4640215E-02 1.007396 at 80iterations 1.7290667E-02 0.5221786 at 90iterations 8.6780461E-03 0.2607632 at 100iterations 4.3310937E-03 0.1367216 at 110iterations 2.1866984E-03 7.5115204E-02 at 120iterations finished qdiffx linear iterations at : 06:35:31 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.1866984E-03 7.5115204E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 06:35:33 7.911u 0.201s 0:09.19 88.2% 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 06:35:33 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 = 2077 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.198498 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): -20.83400 23.85900 ymin,ymax (A): -28.61700 10.96900 zmin,zma (A): -13.45800 36.62800 x,y,z range (A): 44.69300 39.58600 50.08600 scale (grids/A): 3.198498 object centre (A): 1.512501 -8.824000 11.58500 number of atom coordinates read : 2077 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 92.27258 93.01898 86.55505 assigned negative charge : -308.6742 centred at (gu) : 91.63536 92.93987 86.20987 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16792 grid for indexing accessible points = 1.400000 m= 94565 mr = 130549 m= 38376 mr = 78961 m= 11185 mr = 31751 m= 2223 mr = 8784 m= 291 mr = 1631 m= 9 mr = 174 m= 0 mr = 3 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 69340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 15592 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) : 2.132332 object centre at (A) : 1.512501 -8.824000 11.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5652358 0.3800622 midg,1,midg; midg,igrid,midg 2.5956588E-02 0.2574713 1,midg,midg; igrid,midg,midg 0.2416324 0.3376072 gauss-seidel spectral radius is 0.9992937 estimated iterations to convergence 297 setup time was (sec) 1.380000 now iterating at: 06:35:35 rms-change max change #iterations 10.21285 411.0341 at 10iterations 6.037295 122.9263 at 20iterations 3.554730 80.81082 at 30iterations 2.093946 48.95844 at 40iterations 1.232306 21.75260 at 50iterations 0.7236205 13.74252 at 60iterations 0.4240725 7.264149 at 70iterations 0.2485505 4.456540 at 80iterations 0.1455688 2.760203 at 90iterations 8.5435100E-02 1.478828 at 100iterations 5.0053783E-02 0.8560419 at 110iterations 2.9427690E-02 0.5549450 at 120iterations 1.7388673E-02 0.3276205 at 130iterations 1.0389439E-02 0.1876736 at 140iterations 6.3375537E-03 0.1113396 at 150iterations 3.9782510E-03 7.3936462E-02 at 160iterations 2.6225608E-03 5.4458618E-02 at 170iterations 1.8219186E-03 3.3096313E-02 at 180iterations finished qdiffx linear iterations at : 06:35:46 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 1.8219186E-03 3.3096313E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 06:35:46 12.662u 0.218s 0:13.42 95.9% 0+0k 0+0io 0pf+0w