Sat Oct 8 15:58:31 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 8 2011 at 15:58:31 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 = 2331 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: 0.6432843 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): -2.392000 46.67700 ymin,ymax (A): 16.74400 62.09400 zmin,zma (A): -18.83300 36.50800 x,y,z range (A): 49.06900 45.35000 55.34100 scale (grids/A): 0.6432843 object centre (A): 22.14250 39.41900 8.837502 number of atom coordinates read : 2331 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 90.42178 88.89254 90.21132 assigned negative charge : -338.3788 centred at (gu) : 90.48430 89.02345 90.23727 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6504 nv = 96 ne = 84 npr = 47347 no. pairs analyzed = 47347 no. exposed pairs = 2912 no. arc points = 20171 no. surface atoms = 995 nbur = 1336 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3601 m= 0 mr = 48 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3300000 number of dielectric boundary points 3209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2023 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7409457E-09 3.5105561E-09 midg,1,midg; midg,igrid,midg 2.6136586E-08 -6.6179910E-09 1,midg,midg; igrid,midg,midg 1.2038494E-08 -8.3853374E-10 gauss-seidel spectral radius is 0.9874567 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 15:58:32 rms-change max change #iterations 0.1380771 19.85705 at 10iterations 1.3932267E-02 2.267139 at 20iterations 1.4913825E-03 0.2226458 at 30iterations 2.0933521E-04 3.5573959E-02 at 40iterations 4.5644232E-05 7.8821182E-03 at 50iterations finished qdiffx linear iterations at : 15:58:35 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 4.5644232E-05 7.8821182E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 15:58:35 4.028u 0.260s 0:04.61 92.8% 0+0k 0+0io 5pf+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 8 2011 at 15:58:35 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 = 2331 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: 1.929853 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): -2.392000 46.67700 ymin,ymax (A): 16.74400 62.09400 zmin,zma (A): -18.83300 36.50800 x,y,z range (A): 49.06900 45.35000 55.34100 scale (grids/A): 1.929853 object centre (A): 22.14250 39.41900 8.837502 number of atom coordinates read : 2331 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.26479 86.67701 90.63358 assigned negative charge : -338.3788 centred at (gu) : 91.45283 87.07048 90.71159 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 70309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20171 grid for indexing accessible points = 1.400000 m= 25684 mr = 49030 m= 4527 mr = 19070 m= 259 mr = 3031 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 406 time to turn everything in is 0.6200000 number of dielectric boundary points 29569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17568 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) : 0.6432843 object centre at (A) : 22.14250 39.41900 8.837502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5968245E-02 -3.2593056E-03 midg,1,midg; midg,igrid,midg 2.8700180E-02 -6.7572733E-03 1,midg,midg; igrid,midg,midg 1.1867921E-02 -3.4698009E-02 gauss-seidel spectral radius is 0.9986422 estimated iterations to convergence 215 setup time was (sec) 0.9100000 now iterating at: 15:58:37 rms-change max change #iterations 4.066787 180.8810 at 10iterations 1.902054 65.51182 at 20iterations 0.8941748 28.37117 at 30iterations 0.4198842 13.97364 at 40iterations 0.1974639 6.721117 at 50iterations 9.2773594E-02 2.778977 at 60iterations 4.3573268E-02 1.342065 at 70iterations 2.0499751E-02 0.6438441 at 80iterations 9.6237808E-03 0.3075638 at 90iterations 4.5402236E-03 0.1487141 at 100iterations 2.1464974E-03 7.4491501E-02 at 110iterations 1.0252172E-03 3.0906677E-02 at 120iterations finished qdiffx linear iterations at : 15:58:45 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 1.0252172E-03 3.0906677E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 15:58:45 9.296u 0.311s 0:09.90 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 Sat Oct 8 2011 at 15:58:45 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 = 2331 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: 2.894779 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): -2.392000 46.67700 ymin,ymax (A): 16.74400 62.09400 zmin,zma (A): -18.83300 36.50800 x,y,z range (A): 49.06900 45.35000 55.34100 scale (grids/A): 2.894779 object centre (A): 22.14250 39.41900 8.837502 number of atom coordinates read : 2331 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.89720 85.01528 90.95027 assigned negative charge : -338.3788 centred at (gu) : 92.17914 85.60574 91.06744 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 162837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20171 grid for indexing accessible points = 1.400000 m= 82172 mr = 118832 m= 30893 mr = 67372 m= 8422 mr = 25208 m= 1331 mr = 6661 m= 49 mr = 954 m= 0 mr = 14 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1304 time to turn everything in is 1.620000 number of dielectric boundary points 66663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 17840 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) : 1.929853 object centre at (A) : 22.14250 39.41900 8.837502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1555573 -0.1227957 midg,1,midg; midg,igrid,midg 0.2385775 -8.7067738E-02 1,midg,midg; igrid,midg,midg 0.1163812 -0.5172216 gauss-seidel spectral radius is 0.9992547 estimated iterations to convergence 289 setup time was (sec) 1.940000 now iterating at: 15:58:48 rms-change max change #iterations 9.515137 443.1343 at 10iterations 5.562394 118.1451 at 20iterations 3.233025 75.77855 at 30iterations 1.876665 36.16626 at 40iterations 1.087525 22.61783 at 50iterations 0.6277564 12.79701 at 60iterations 0.3625109 7.002583 at 70iterations 0.2091704 3.907478 at 80iterations 0.1205190 2.189886 at 90iterations 6.9274075E-02 1.440356 at 100iterations 3.9838437E-02 0.7561100 at 110iterations 2.2966057E-02 0.4244080 at 120iterations 1.3211215E-02 0.2613297 at 130iterations 7.6242895E-03 0.1348591 at 140iterations 4.4153952E-03 8.1537247E-02 at 150iterations 2.5779216E-03 4.5808792E-02 at 160iterations 1.5246536E-03 3.1078339E-02 at 170iterations 9.2242315E-04 1.8568039E-02 at 180iterations finished qdiffx linear iterations at : 15:59:01 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 9.2242315E-04 1.8568039E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 15:59:02 15.543u 0.311s 0:16.16 98.0% 0+0k 0+0io 0pf+0w